ENCODE RNA Dashboard (mm9)

Tissues

Compartments

RNA Fractions

10T1/2 Strain: C3H Age: immortalized Sex: F

2

10T1/2, C3H, immortalized, F, RnaSeq (Hardison), longPolyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Insert Length	Treatment	bai	bam	bigWig	fastq
Caltech	1	11154	2x75	200	None	Alignments Unrestricted date: 2012-12-20	Alignments Unrestricted date: 2012-12-20	RawSignal Unrestricted date: 2013-01-16 Signal Unrestricted date: 2012-12-20	FastqRd1 Unrestricted date: 2012-12-20 FastqRd2 Unrestricted date: 2012-12-20
Caltech	1	11155	2x75	200	EqS_2.0pct_60hr	Alignments Unrestricted date: 2012-12-19	Alignments Unrestricted date: 2012-12-19	RawSignal Unrestricted date: 2013-01-16 Signal Unrestricted date: 2012-12-19	FastqRd1 Unrestricted date: 2012-12-19 FastqRd2 Unrestricted date: 2012-12-19

longPolyA

polyA

riboZeroGold

total

416B Strain: B6D2F1/J Age: immortalized Sex: M

longPolyA

2

416B, B6D2F1/J, immortalized, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jRep1	1x50		Alignments Unrestricted date: 2012-03-24	Alignments Unrestricted date: 2012-03-24
UW	2	wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jRep2	1x50		Alignments Unrestricted date: 2012-03-24	Alignments Unrestricted date: 2012-03-24
UW	1,2	wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jRep1,wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jRep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

A20 Strain: BALB/cAnN Age: immortalized Sex: M

longPolyA

2

A20, BALB/cAnN, immortalized, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannRep1	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	2	wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannRep2	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	1,2	wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannRep1,wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannRep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Adrenal Strain: C57BL/6J Age: adult-8wks Sex: U

2

Adrenal, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20728	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20729	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20728,LID20729	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

B-cell_(CD19+) Strain: C57BL/6 Age: adult-8wks Sex: M

longPolyA

1

B-cell_(CD19+), C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment		bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6Rep1	1x50			Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22	ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

B-cell_(CD43-) Strain: C57BL/6 Age: adult-8wks Sex: M

longPolyA

2

B-cell_(CD43-), C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	2	wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	1,2	wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6Rep1,wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

BAT Strain: C57BL/6 Age: adult-24wks Sex: M

2

BAT, C57BL/6, adult-24wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-12-08	Alignments Unrestricted date: 2012-12-08
LICR	2	wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-12-08	Alignments Unrestricted date: 2012-12-08
LICR	1,2	wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6Rep1,wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

BMDM Strain: C57BL/6 Age: adult-8wks Sex: F

2

BMDM, C57BL/6, adult-8wks, F, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6Rep1	1x30		Alignments Unrestricted date: 2012-12-09	Alignments Unrestricted date: 2012-12-09
LICR	2	wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6Rep2	1x30		Alignments Unrestricted date: 2012-12-09	Alignments Unrestricted date: 2012-12-09
LICR	1,2	wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6Rep2	1x30	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

Bladder Strain: C57BL/6J Age: adult-8wks Sex: U

2

Bladder, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID47030	2x101D	Alignments Unrestricted date: 2013-04-14	Alignments Unrestricted date: 2013-04-14		MinusRawSignal Unrestricted date: 2013-04-14 PlusRawSignal Unrestricted date: 2013-04-14	FastqRd1 Unrestricted date: 2013-04-14 FastqRd2 Unrestricted date: 2013-04-14		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID47031	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID47030,LID47031	2x101D			Contigs Unrestricted date: 2013-04-13 Junctions Unrestricted date: 2013-04-13			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

BoneMarrow Strain: C57BL/6 Age: adult-8wks Sex: M

2

BoneMarrow, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6Rep1	1x30		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	2	wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6Rep2	1x30		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	1,2	wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6Rep2	1x30	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

C2C12 Strain: C3H Age: immortalized Sex: F

2

C2C12, C3H, immortalized, F, RnaSeq (Hardison), longPolyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Insert Length	Treatment	bai	bam	bigWig	fastq
Caltech	1	10985	2x75	200	None	Alignments Unrestricted date: 2012-10-31	Alignments Unrestricted date: 2012-10-31	RawSignal Unrestricted date: 2013-01-16 Signal Unrestricted date: 2012-11-31	FastqRd1 Unrestricted date: 2012-10-31 FastqRd2 Unrestricted date: 2012-10-31
Caltech	1	10986	2x75	200	EqS_2.0pct_60hr	Alignments Unrestricted date: 2012-10-31	Alignments Unrestricted date: 2012-10-31	RawSignal Unrestricted date: 2013-01-16 Signal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01

longPolyA

polyA

riboZeroGold

total

CH12 Strain: B10.H-2aH-4bp/Wts Age: immortalized Sex: F

longPolyA

2

CH12, B10.H-2aH-4bp/Wts, immortalized, F, RnaSeq (Hardison), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
PSU	1	wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41Rep1	1x41	None	Alignments Unrestricted date: 2012-12-28	Alignments Unrestricted date: 2012-12-28
PSU	2	wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41Rep2	1x41	None	Alignments Unrestricted date: 2012-12-28	Alignments Unrestricted date: 2012-12-28
PSU	1,2	wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41Rep1,wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41Rep2	1x41	None			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

2

CH12, B10.H-2aH-4bp/Wts, immortalized, F, RnaSeq (Snyder), riboZeroGold, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
Stanford	1	wgEncodeSydhRnaSeqCh12RibozerogR2x101dRep1	2x101D	None	Alignments Unrestricted date: 2013-01-19	Alignments Unrestricted date: 2013-01-19
Stanford	2	wgEncodeSydhRnaSeqCh12RibozerogR2x101dRep2	2x101D	None	Alignments Unrestricted date: 2013-01-19	Alignments Unrestricted date: 2013-01-19
Stanford	1,2	wgEncodeSydhRnaSeqCh12RibozerogR2x101dRep1,wgEncodeSydhRnaSeqCh12RibozerogR2x101dRep2	2x101D	None			ExonsEnsV65 Unrestricted date: None GeneEnsV65 Unrestricted date: None	TranscriptEnsV65 Unrestricted date: None

riboZeroGold

total

CH12 Strain: CH12 Age: adult-8wks Sex: U

2

CH12, CH12, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bam	bigWig	fastq	gff	gtf
CSHL	1	SID38132	2x101D	Alignments Unrestricted date: None Spikeins Unrestricted date: None	MinusRawSignal Unrestricted date: None PlusRawSignal Unrestricted date: None	FastqRd1 Unrestricted date: None FastqRd2 Unrestricted date: None
CSHL	2	SID38133	2x101D	Alignments Unrestricted date: None Spikeins Unrestricted date: None	MinusRawSignal Unrestricted date: None PlusRawSignal Unrestricted date: None	FastqRd1 Unrestricted date: None FastqRd2 Unrestricted date: None
CSHL	1,2	SID38132,SID38133	2x101D				ExonsEnsV65 Unrestricted date: None GeneEnsV65 Unrestricted date: None	TranscriptEnsV65 Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

CNS Strain: C57BL/6J Age: E11.5 Sex: U

2

CNS, C57BL/6J, E11.5, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID46946	2x101D	Alignments Unrestricted date: 2013-04-14	Alignments Unrestricted date: 2013-04-14		MinusRawSignal Unrestricted date: 2013-04-14 PlusRawSignal Unrestricted date: 2013-04-14	FastqRd1 Unrestricted date: 2013-04-14 FastqRd2 Unrestricted date: 2013-04-14		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID46947	2x101D	Alignments Unrestricted date: 2013-04-11	Alignments Unrestricted date: 2013-04-11		MinusRawSignal Unrestricted date: 2013-04-11 PlusRawSignal Unrestricted date: 2013-04-11	FastqRd1 Unrestricted date: 2013-04-11 FastqRd2 Unrestricted date: 2013-04-11		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID46946,LID46947	2x101D			Contigs Unrestricted date: 2013-04-13 Junctions Unrestricted date: 2013-04-13			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

CNS Strain: C57BL/6J Age: E14 Sex: U

2

CNS, C57BL/6J, E14, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID46948	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID46949	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID46948,LID46949	2x101D			Contigs Unrestricted date: 2013-04-13 Junctions Unrestricted date: 2013-04-13			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

CNS Strain: C57BL/6J Age: E18 Sex: U

2

CNS, C57BL/6J, E18, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID46950	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID46951	2x101D	Alignments Unrestricted date: 2013-04-14	Alignments Unrestricted date: 2013-04-14		MinusRawSignal Unrestricted date: 2013-04-14 PlusRawSignal Unrestricted date: 2013-04-14	FastqRd1 Unrestricted date: 2013-04-14 FastqRd2 Unrestricted date: 2013-04-14		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID46950,LID46951	2x101D			Contigs Unrestricted date: 2013-04-13 Junctions Unrestricted date: 2013-04-13			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

Cerebellum Strain: C57BL/6 Age: adult-8wks Sex: M

2

Cerebellum, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	2	wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	1,2	wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

2

Cerebellum, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	2	wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-11-12	Alignments Unrestricted date: 2012-11-12
UW	1,2	wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6Rep1,wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Cerebellum Strain: C57BL/6J Age: adult-8wks Sex: U

2

Cerebellum, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID47036	2x101D	Alignments Unrestricted date: 2013-04-14	Alignments Unrestricted date: 2013-04-14		MinusRawSignal Unrestricted date: 2013-04-14 PlusRawSignal Unrestricted date: 2013-04-14	FastqRd1 Unrestricted date: 2013-04-14 FastqRd2 Unrestricted date: 2013-04-14		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID47037	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID47036,LID47037	2x101D			Contigs Unrestricted date: 2013-04-14 Junctions Unrestricted date: 2013-04-14			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

Cerebrum Strain: C57BL/6 Age: adult-8wks Sex: M

longPolyA

2

Cerebrum, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	2	wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	1,2	wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6Rep1,wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Colon Strain: C57BL/6J Age: adult-8wks Sex: U

2

Colon, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID21040	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID21041	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID21040,LID21041	2x76D			Contigs Unrestricted date: 2012-11-08 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-08 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

Cortex Strain: C57BL/6 Age: adult-8wks Sex: M

2

Cortex, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	2	wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	1,2	wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

Cortex Strain: C57BL/6J Age: adult-8wks Sex: U

2

Cortex, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID47032	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID47033	2x101D	Alignments Unrestricted date: 2013-04-14	Alignments Unrestricted date: 2013-04-14		MinusRawSignal Unrestricted date: 2013-04-14 PlusRawSignal Unrestricted date: 2013-04-14	FastqRd1 Unrestricted date: 2013-04-14 FastqRd2 Unrestricted date: 2013-04-14		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID47032,LID47033	2x101D			Contigs Unrestricted date: 2013-04-13 Junctions Unrestricted date: 2013-04-13			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

Duodenum Strain: C57BL/6J Age: adult-8wks Sex: U

2

Duodenum, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20730	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20731	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20730,LID20731	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

ES-Bruce4 Strain: C57BL/6 Age: E0 Sex: M

2

ES-Bruce4, C57BL/6, E0, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6Rep1	1x30		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	2	wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6Rep2	1x30		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	1,2	wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6Rep1,wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6Rep2	1x30	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

ES-E14 Strain: 129/Ola Age: E0 Sex: M

longPolyA

polyA

2

ES-E14, 129/Ola, E0, M, RnaSeq (Snyder), riboZeroGold, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
Stanford	1	wgEncodeSydhRnaSeqEse14RibozerogR2x101dRep1	2x101D	None	Alignments Unrestricted date: 2013-01-19	Alignments Unrestricted date: 2013-01-19
Stanford	2	wgEncodeSydhRnaSeqEse14RibozerogR2x101dRep2	2x101D	None	Alignments Unrestricted date: 2013-01-19	Alignments Unrestricted date: 2013-01-19
Stanford	1,2	wgEncodeSydhRnaSeqEse14RibozerogR2x101dRep1,wgEncodeSydhRnaSeqEse14RibozerogR2x101dRep2	2x101D	None			ExonsEnsV65 Unrestricted date: None GeneEnsV65 Unrestricted date: None	TranscriptEnsV65 Unrestricted date: None

riboZeroGold

total

Erythrobl Strain: CD-1 Age: E14.5 Sex: B

longPolyA

2

Erythrobl, CD-1, E14.5, B, RnaSeq (Hardison), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam
PSU	1	wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dRep1	2x99D	None	Alignments Unrestricted date: 2013-04-20	Alignments Unrestricted date: 2013-04-20
PSU	2	wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dRep2	2x99D	None	Alignments Unrestricted date: 2013-04-20	Alignments Unrestricted date: 2013-04-20

polyA

riboZeroGold

total

FVLstem Strain: BALB/cJ Age: adult-10-12wks Sex: B

longPolyA

2

FVLstem, BALB/cJ, adult-10-12wks, B, RnaSeq (Hardison), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam
PSU	1	wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dRep1	2x99D	None	Alignments Unrestricted date: 2013-04-22	Alignments Unrestricted date: 2013-04-22
PSU	2	wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dRep2	2x99D	None	Alignments Unrestricted date: 2013-04-22	Alignments Unrestricted date: 2013-04-22

polyA

riboZeroGold

total

FVprogenitor Strain: BALB/cJ Age: adult-10-12wks Sex: B

longPolyA

2

FVprogenitor, BALB/cJ, adult-10-12wks, B, RnaSeq (Hardison), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam
PSU	1	wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dRep1	2x99D	None	Alignments Unrestricted date: 2013-04-20	Alignments Unrestricted date: 2013-04-20
PSU	2	wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dRep2	2x99D	None	Alignments Unrestricted date: 2013-04-20	Alignments Unrestricted date: 2013-04-20

polyA

riboZeroGold

total

FatPad Strain: C57BL/6 Age: adult-8wks Sex: M

longPolyA

1

FatPad, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment		bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6Rep1	1x50			Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28	ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

FrontalLobe Strain: C57BL/6J Age: adult-8wks Sex: U

2

FrontalLobe, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID47081	2x101D	Alignments Unrestricted date: 2013-04-14	Alignments Unrestricted date: 2013-04-14		MinusRawSignal Unrestricted date: 2013-04-14 PlusRawSignal Unrestricted date: 2013-04-14	FastqRd1 Unrestricted date: 2013-04-14 FastqRd2 Unrestricted date: 2013-04-14		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID47082	2x101D	Alignments Unrestricted date: 2013-04-14	Alignments Unrestricted date: 2013-04-14		MinusRawSignal Unrestricted date: 2013-04-14 PlusRawSignal Unrestricted date: 2013-04-14	FastqRd1 Unrestricted date: 2013-04-14 FastqRd2 Unrestricted date: 2013-04-14		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID47081,LID47082	2x101D			Contigs Unrestricted date: 2013-04-14 Junctions Unrestricted date: 2013-04-14			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

G1E Strain: 129 Age: E0 Sex: M

longPolyA

4

G1E, 129, E0, M, RnaSeq (Hardison), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
PSU	1	wgEncodePsuRnaSeqG1eME0S129R1x36Rep1	1x36	None	Alignments Unrestricted date: 2012-12-28	Alignments Unrestricted date: 2012-12-28
PSU	2	wgEncodePsuRnaSeqG1eME0S129R1x55Rep2	1x55	None	Alignments Unrestricted date: 2012-12-28	Alignments Unrestricted date: 2012-12-28
PSU	1	wgEncodePsuRnaSeqG1eME0S129R2x99dRep1	2x99D	None	Alignments Unrestricted date: 2013-04-22	Alignments Unrestricted date: 2013-04-22
PSU	2	wgEncodePsuRnaSeqG1eME0S129R2x99dRep2	2x99D	None	Alignments Unrestricted date: 2013-04-22	Alignments Unrestricted date: 2013-04-22
PSU	1,2	wgEncodePsuRnaSeqG1eME0S129R1x36Rep1,wgEncodePsuRnaSeqG1eME0S129R1x55Rep2	1x36,1x55	None			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

G1E-ER4 Strain: 129 Age: E0 Sex: M

longPolyA

14

G1E-ER4, 129, E0, M, RnaSeq (Hardison), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
PSU	1	wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hRep1	1x36	diffProtD_24hr	Alignments Unrestricted date: 2012-12-28	Alignments Unrestricted date: 2012-12-28
PSU	2	wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hRep2	1x36	diffProtD_24hr	Alignments Unrestricted date: 2012-12-28	Alignments Unrestricted date: 2012-12-28
PSU	1	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dRep1	2x99D	None	Alignments Unrestricted date: 2013-04-25	Alignments Unrestricted date: 2013-04-25
PSU	2	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dRep2	2x99D	None	Alignments Unrestricted date: 2013-04-25	Alignments Unrestricted date: 2013-04-25
PSU	1	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hRep1	2x99D	diffProtD_14hr	Alignments Unrestricted date: 2013-04-24	Alignments Unrestricted date: 2013-04-24
PSU	2	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hRep2	2x99D	diffProtD_14hr	Alignments Unrestricted date: 2013-04-24	Alignments Unrestricted date: 2013-04-24
PSU	1	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hRep1	2x99D	diffProtD_24hr	Alignments Unrestricted date: 2013-04-25	Alignments Unrestricted date: 2013-04-25
PSU	2	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hRep2	2x99D	diffProtD_24hr	Alignments Unrestricted date: 2013-04-25	Alignments Unrestricted date: 2013-04-25
PSU	1	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hRep1	2x99D	diffProtD_30hr	Alignments Unrestricted date: 2013-04-27	Alignments Unrestricted date: 2013-04-27
PSU	2	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hRep2	2x99D	diffProtD_30hr	Alignments Unrestricted date: 2013-04-27	Alignments Unrestricted date: 2013-04-27
PSU	1	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hRep1	2x99D	diffProtD_3hr	Alignments Unrestricted date: 2013-04-25	Alignments Unrestricted date: 2013-04-25
PSU	2	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hRep2	2x99D	diffProtD_3hr	Alignments Unrestricted date: 2013-04-25	Alignments Unrestricted date: 2013-04-25
PSU	1	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hRep1	2x99D	diffProtD_7hr	Alignments Unrestricted date: 2013-04-24	Alignments Unrestricted date: 2013-04-24
PSU	2	wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hRep2	2x99D	diffProtD_7hr	Alignments Unrestricted date: 2013-04-24	Alignments Unrestricted date: 2013-04-24
PSU	1,2	wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hRep1,wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hRep2	1x36	diffProtD_24hr			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

GenitalFatPad Strain: C57BL/6 Age: adult-8wks Sex: M

longPolyA

2

GenitalFatPad, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	2	wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	1,2	wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6Rep1,wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

GenitalFatPad Strain: C57BL/6J Age: adult-8wks Sex: U

2

GenitalFatPad, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID21179	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID21180	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID21179,LID21180	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

HeadlessEmbryo Strain: CD-1 Age: E11.5 Sex: M

longPolyA

1

HeadlessEmbryo, CD-1, E11.5, M, RnaSeq (Stam), polyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment		bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1Rep1	1x50			Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28	ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Heart Strain: C57BL/6 Age: E14.5 Sex: U

2

Heart, C57BL/6, E14.5, U, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-10-04	Alignments Unrestricted date: 2012-10-04
LICR	2	wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-10-04	Alignments Unrestricted date: 2012-10-04
LICR	1,2	wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6Rep1,wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

Heart Strain: C57BL/6 Age: adult-8wks Sex: M

2

Heart, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	2	wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	1,2	wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

2

Heart, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	2	wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	1,2	wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6Rep1,wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Heart Strain: C57BL/6J Age: adult-8wks Sex: U

2

Heart, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20870	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20871	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20870,LID20871	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

Kidney Strain: C57BL/6 Age: adult-8wks Sex: M

2

Kidney, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	2	wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	1,2	wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

1

Kidney, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment		bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6Rep1	1x50			Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28	ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Kidney Strain: C57BL/6J Age: adult-8wks Sex: U

2

Kidney, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20872	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20873	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20872,LID20873	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

LgIntestine Strain: C57BL/6 Age: adult-8wks Sex: M

longPolyA

2

LgIntestine, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	2	wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	1,2	wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6Rep1,wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

LgIntestine Strain: C57BL/6J Age: adult-8wks Sex: U

2

LgIntestine, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID21183	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID21184	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID21183,LID21184	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

Limb Strain: C57BL/6 Age: E14.5 Sex: U

2

Limb, C57BL/6, E14.5, U, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-10-03	Alignments Unrestricted date: 2012-10-03
LICR	2	wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-10-03	Alignments Unrestricted date: 2012-10-03
LICR	1,2	wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6Rep1,wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

Limb Strain: C57BL/6J Age: E14.5 Sex: U

2

Limb, C57BL/6J, E14.5, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID46985	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID46986	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID46985,LID46986	2x101D			Contigs Unrestricted date: 2013-04-14 Junctions Unrestricted date: 2013-04-14			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

Liver Strain: 129 Age: E14.5 Sex: M

longPolyA

1

Liver, 129, E14.5, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type		bai	bam
UW	1	wgEncodeUwRnaSeqLiverCellPolyaME14halfS129Rep1	1x50		Alignments Unrestricted date: 2012-11-12	Alignments Unrestricted date: 2012-11-12

polyA

riboZeroGold

total

Liver Strain: C57BL/6 Age: E14.5 Sex: M

longPolyA

1

Liver, C57BL/6, E14.5, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type		bai	bam
UW	1	wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28

polyA

riboZeroGold

total

Liver Strain: C57BL/6 Age: E14.5 Sex: U

2

Liver, C57BL/6, E14.5, U, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-10-04	Alignments Unrestricted date: 2012-10-04
LICR	2	wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-10-04	Alignments Unrestricted date: 2012-10-04
LICR	1,2	wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6Rep1,wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

Liver Strain: C57BL/6 Age: adult-8wks Sex: M

2

Liver, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	2	wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	1,2	wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

4

Liver, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	2	wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	3	wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6Rep3	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	4	wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6Rep4	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	1,2	wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6Rep1,wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None
UW	3,4	wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6Rep3,wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6Rep4	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Liver Strain: C57BL/6,129 Age: E14.5 Sex: M

longPolyA

2

Liver, C57BL/6,129, E14.5, M, RnaSeq (Stam), polyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment		gff	gtf
UW	1	wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6Rep1,wgEncodeUwRnaSeqLiverCellPolyaME14halfS129Rep1	1x50	.		ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Liver Strain: C57BL/6J Age: E14 Sex: U

2

Liver, C57BL/6J, E14, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID47144	2x101D	Alignments Unrestricted date: 2013-04-11	Alignments Unrestricted date: 2013-04-11		MinusRawSignal Unrestricted date: 2013-04-11 PlusRawSignal Unrestricted date: 2013-04-11	FastqRd1 Unrestricted date: 2013-04-11 FastqRd2 Unrestricted date: 2013-04-11		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID47145	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID47144,LID47145	2x101D			Contigs Unrestricted date: 2013-04-14 Junctions Unrestricted date: 2013-04-14			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

Liver Strain: C57BL/6J Age: E14.5 Sex: U

2

Liver, C57BL/6J, E14.5, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID47146	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID47147	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID47146,LID47147	2x101D			Contigs Unrestricted date: 2013-04-11 Junctions Unrestricted date: 2013-04-11			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

Liver Strain: C57BL/6J Age: E18 Sex: U

2

Liver, C57BL/6J, E18, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID47148	2x101D	Alignments Unrestricted date: 2013-04-14	Alignments Unrestricted date: 2013-04-14		MinusRawSignal Unrestricted date: 2013-04-14 PlusRawSignal Unrestricted date: 2013-04-14	FastqRd1 Unrestricted date: 2013-04-14 FastqRd2 Unrestricted date: 2013-04-14		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID47149	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID47148,LID47149	2x101D			Contigs Unrestricted date: 2013-04-14 Junctions Unrestricted date: 2013-04-14			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

Liver Strain: C57BL/6J Age: adult-8wks Sex: U

2

Liver, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID21042	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID21043	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID21042,LID21043	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

2

Liver, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), total, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bam	bigWig	fastq	gff	gtf
CSHL	1	SID38134	2x101D	Alignments Unrestricted date: None Spikeins Unrestricted date: None	MinusRawSignal Unrestricted date: None PlusRawSignal Unrestricted date: None	FastqRd1 Unrestricted date: None FastqRd2 Unrestricted date: None
CSHL	1,2	SID38134,SID38135	2x101D				ExonsEnsV65 Unrestricted date: None GeneEnsV65 Unrestricted date: None	TranscriptEnsV65 Unrestricted date: None
CSHL	2	SID38135	2x101D	Alignments Unrestricted date: None Spikeins Unrestricted date: None	MinusRawSignal Unrestricted date: None PlusRawSignal Unrestricted date: None	FastqRd1 Unrestricted date: None FastqRd2 Unrestricted date: None

total

Lung Strain: C57BL/6 Age: adult-8wks Sex: M

2

Lung, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	2	wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	1,2	wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

1

Lung, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment		bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6Rep1	1x50			Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22	ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Lung Strain: C57BL/6J Age: adult-8wks Sex: U

2

Lung, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20920	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20921	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20920,LID20921	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

MEF Strain: C57BL/6 Age: adult-8wks Sex: M

2

MEF, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	2	wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	1,2	wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

MEL Strain: C57BL/6 Age: adult-8wks Sex: M

longPolyA

2

MEL, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment		gff	gtf
UW	1,2	wgEncodeUwRnaSeqMelCellPolyaMImmortalUknRep1,wgEncodeUwRnaSeqMelCellPolyaMImmortalUknRep2	1x50	.		ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

MEL Strain: C57BL/6 Age: immortalized Sex: M

2

MEL, C57BL/6, immortalized, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment		gff	gtf
LICR	1,2	wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6Rep1,wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6Rep2	1x36	.		ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

MEL Strain: Unknown Age: adult-8wks Sex: M

longPolyA

2

MEL, Unknown, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam
UW	1	wgEncodeUwRnaSeqMelCellPolyaMImmortalUknRep1	1x50	Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	2	wgEncodeUwRnaSeqMelCellPolyaMImmortalUknRep2	1x50	Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28

polyA

riboZeroGold

total

MEL Strain: Unknown Age: immortalized Sex: M

2

MEL, Unknown, immortalized, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam
LICR	1	wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6Rep1	1x36	Alignments Unrestricted date: 2012-11-29	Alignments Unrestricted date: 2012-11-29
LICR	2	wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6Rep2	1x36	Alignments Unrestricted date: 2012-11-29	Alignments Unrestricted date: 2012-11-29

longPolyA

4

MEL, Unknown, immortalized, M, RnaSeq (Hardison), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam
PSU	1	wgEncodePsuRnaSeqMelMImmortalUknR1x45Rep1	1x45	None	Alignments Unrestricted date: 2013-04-26	Alignments Unrestricted date: 2013-04-26
PSU	2	wgEncodePsuRnaSeqMelMImmortalUknR1x45Rep2	1x45	None	Alignments Unrestricted date: 2013-04-26	Alignments Unrestricted date: 2013-04-26
PSU	1	wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dRep1	1x45	DMSO_2.0pct	Alignments Unrestricted date: 2013-04-26	Alignments Unrestricted date: 2013-04-26
PSU	2	wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dRep2	1x45	DMSO_2.0pct	Alignments Unrestricted date: 2013-04-26	Alignments Unrestricted date: 2013-04-26

polyA

4

MEL, Unknown, immortalized, M, RnaSeq (Snyder), riboZeroGold, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
Stanford	1	wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dRep1	2x101D	DMSO_2.0pct	Alignments Unrestricted date: 2013-01-19	Alignments Unrestricted date: 2013-01-19
Stanford	2	wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dRep2	2x101D	DMSO_2.0pct	Alignments Unrestricted date: 2013-01-19	Alignments Unrestricted date: 2013-01-19
Stanford	1	wgEncodeSydhRnaSeqMelRibozerogR2x101dRep1	2x101D	None	Alignments Unrestricted date: 2013-02-01	Alignments Unrestricted date: 2013-02-01
Stanford	2	wgEncodeSydhRnaSeqMelRibozerogR2x101dRep2	2x101D	None	Alignments Unrestricted date: 2013-02-01	Alignments Unrestricted date: 2013-02-01
Stanford	1,2	wgEncodeSydhRnaSeqMelRibozerogR2x101dRep1,wgEncodeSydhRnaSeqMelRibozerogR2x101dRep2	2x101D	None			ExonsEnsV65 Unrestricted date: None GeneEnsV65 Unrestricted date: None	TranscriptEnsV65 Unrestricted date: None

riboZeroGold

total

MEP Strain: C57BL/6J Age: adult-5wks Sex: F

longPolyA

2

MEP, C57BL/6J, adult-5wks, F, RnaSeq (Hardison), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam
PSU	1	wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dRep1	2x99D	None	Alignments Unrestricted date: 2013-04-22	Alignments Unrestricted date: 2013-04-22
PSU	2	wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dRep2	2x99D	None	Alignments Unrestricted date: 2013-04-22	Alignments Unrestricted date: 2013-04-22

polyA

riboZeroGold

total

MammaryGland Strain: C57BL/6J Age: adult-8wks Sex: U

2

MammaryGland, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20924	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20925	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-02 PlusRawSignal Unrestricted date: 2012-11-02	FastqRd1 Unrestricted date: 2012-11-02 FastqRd2 Unrestricted date: 2012-11-02		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20924,LID20925	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

Megakaryo Strain: CD-1 Age: E14.5 Sex: B

longPolyA

2

Megakaryo, CD-1, E14.5, B, RnaSeq (Hardison), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam
PSU	1	wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dRep1	2x99D	None	Alignments Unrestricted date: 2013-04-28	Alignments Unrestricted date: 2013-04-28
PSU	2	wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dRep2	2x99D	None	Alignments Unrestricted date: 2013-04-28	Alignments Unrestricted date: 2013-04-28

polyA

riboZeroGold

total

NIH-3T3 Strain: NIH/Swiss Age: immortalized Sex: M

longPolyA

2

NIH-3T3, NIH/Swiss, immortalized, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsRep1	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	2	wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsRep2	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	1,2	wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsRep1,wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsRep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

OlfactBulb Strain: C57BL/6 Age: adult-8wks Sex: M

2

OlfactBulb, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-09-20	Alignments Unrestricted date: 2012-09-20
LICR	2	wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-09-20	Alignments Unrestricted date: 2012-09-20
LICR	1,2	wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

Ovary Strain: C57BL/6J Age: adult-8wks Sex: U

2

Ovary, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20821	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-02 PlusRawSignal Unrestricted date: 2012-11-02	FastqRd1 Unrestricted date: 2012-11-02 FastqRd2 Unrestricted date: 2012-11-02		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20822	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20821,LID20822	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

Patski Strain: Spretus.BL6-Xist Age: immortalized Sex: F

longPolyA

2

Patski, Spretus.BL6-Xist, immortalized, F, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6Rep1	1x50		Alignments Unrestricted date: 2012-03-29	Alignments Unrestricted date: 2012-03-29
UW	2	wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6Rep2	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	1,2	wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6Rep1,wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Placenta Strain: C57BL/6 Age: adult-8wks Sex: F

2

Placenta, C57BL/6, adult-8wks, F, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-10-05	Alignments Unrestricted date: 2012-10-05
LICR	2	wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-10-05	Alignments Unrestricted date: 2012-10-05
LICR	1,2	wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

Placenta Strain: C57BL/6J Age: adult-8wks Sex: U

2

Placenta, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID46983	2x101D	Alignments Unrestricted date: 2013-04-13	Alignments Unrestricted date: 2013-04-13		MinusRawSignal Unrestricted date: 2013-04-13 PlusRawSignal Unrestricted date: 2013-04-13	FastqRd1 Unrestricted date: 2013-04-13 FastqRd2 Unrestricted date: 2013-04-13		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID46984	2x101D	Alignments Unrestricted date: 2013-04-14	Alignments Unrestricted date: 2013-04-14		MinusRawSignal Unrestricted date: 2013-04-14 PlusRawSignal Unrestricted date: 2013-04-14	FastqRd1 Unrestricted date: 2013-04-14 FastqRd2 Unrestricted date: 2013-04-14		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID46983,LID46984	2x101D			Contigs Unrestricted date: 2013-04-13 Junctions Unrestricted date: 2013-04-13			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

SkMuscle Strain: C57BL/6 Age: adult-8wks Sex: M

longPolyA

2

SkMuscle, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	2	wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	1,2	wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6Rep1,wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

SmIntestine Strain: C57BL/6 Age: adult-8wks Sex: M

2

SmIntestine, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-10-03	Alignments Unrestricted date: 2012-10-03
LICR	2	wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-10-03	Alignments Unrestricted date: 2012-10-03
LICR	1,2	wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

SmIntestine Strain: C57BL/6J Age: adult-8wks Sex: U

2

SmIntestine, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20819	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20820	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20819,LID20820	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

Spleen Strain: C57BL/6 Age: adult-8wks Sex: M

2

Spleen, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	2	wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-02-11	Alignments Unrestricted date: 2012-02-11
LICR	1,2	wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

1

Spleen, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment		bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6Rep1	1x50			Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22	ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Spleen Strain: C57BL/6J Age: adult-8wks Sex: U

2

Spleen, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID21038	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID21039	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID21038,LID21039	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

Stomach Strain: C57BL/6J Age: adult-8wks Sex: U

2

Stomach, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20732	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20733	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20732,LID20733	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

SubcFatPad Strain: C57BL/6J Age: adult-8wks Sex: U

2

SubcFatPad, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID21181	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID21182	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-11-01 PlusRawSignal Unrestricted date: 2012-11-01	FastqRd1 Unrestricted date: 2012-11-01 FastqRd2 Unrestricted date: 2012-11-01		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID21181,LID21182	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

T-Naive Strain: C57BL/6 Age: adult-8wks Sex: M

longPolyA

1

T-Naive, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment						Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment		bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6Rep1	1x50			Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22	ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Testis Strain: C57BL/6 Age: adult-8wks Sex: M

2

Testis, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-10-03	Alignments Unrestricted date: 2012-10-03
LICR	2	wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-10-03	Alignments Unrestricted date: 2012-10-03
LICR	1,2	wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

Testis Strain: C57BL/6J Age: adult-8wks Sex: M

2

Testis, C57BL/6J, adult-8wks, M, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20868	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20869	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-10 PlusRawSignal Unrestricted date: 2012-10-10	FastqRd1 Unrestricted date: 2012-10-10 FastqRd2 Unrestricted date: 2012-10-10		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20868,LID20869	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

Thymus Strain: C57BL/6 Age: adult-8wks Sex: M

2

Thymus, C57BL/6, adult-8wks, M, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-09-20	Alignments Unrestricted date: 2012-09-20
LICR	2	wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-09-20	Alignments Unrestricted date: 2012-09-20
LICR	1,2	wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6Rep1,wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

2

Thymus, C57BL/6, adult-8wks, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	2	wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-09-22	Alignments Unrestricted date: 2012-09-22
UW	1,2	wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6Rep1,wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

Thymus Strain: C57BL/6J Age: adult-8wks Sex: U

2

Thymus, C57BL/6J, adult-8wks, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID20922	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	2	LID20923	2x76D	Alignments Unrestricted date: 2013-04-29	Alignments Unrestricted date: 2013-04-29		MinusRawSignal Unrestricted date: 2012-10-05 PlusRawSignal Unrestricted date: 2012-10-05	FastqRd1 Unrestricted date: 2012-10-05 FastqRd2 Unrestricted date: 2012-10-05		Spikeins Unrestricted date: 2013-04-29
CSHL	1,2	LID20922,LID20923	2x76D			Contigs Unrestricted date: 2012-11-09 Junctions Unrestricted date: 2012-12-23			ExonsDeNovo Unrestricted date: 2013-03-19 ExonsEnsV65IAcuff Unrestricted date: 2012-12-26 GeneDeNovo Unrestricted date: 2013-03-19 GeneEnsV65IAcuff Unrestricted date: 2012-12-26 TranscriptDeNovo Unrestricted date: 2012-11-09 TranscriptEnsV65IAcuff Unrestricted date: 2012-12-26

longPolyA

polyA

riboZeroGold

total

WholeBrain Strain: C57BL/6 Age: E14.5 Sex: M

longPolyA

2

WholeBrain, C57BL/6, E14.5, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	2	wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-03-28	Alignments Unrestricted date: 2012-03-28
UW	1,2	wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6Rep1,wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

WholeBrain Strain: C57BL/6 Age: E14.5 Sex: U

2

WholeBrain, C57BL/6, E14.5, U, RnaSeq (Ren), longPolyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
LICR	1	wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6Rep1	1x36		Alignments Unrestricted date: 2012-10-03	Alignments Unrestricted date: 2012-10-03
LICR	2	wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6Rep2	1x36		Alignments Unrestricted date: 2012-10-03	Alignments Unrestricted date: 2012-10-03
LICR	1,2	wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6Rep1,wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6Rep2	1x36	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

longPolyA

polyA

riboZeroGold

total

WholeBrain Strain: C57BL/6 Age: E18.5 Sex: M

longPolyA

2

WholeBrain, C57BL/6, E18.5, M, RnaSeq (Stam), polyA, Whole-cell

Experiment					Data files
Lab	Biological Replicate	Internal Name	Read Type	Treatment	bai	bam	gff	gtf
UW	1	wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6Rep1	1x50		Alignments Unrestricted date: 2012-03-29	Alignments Unrestricted date: 2012-03-29
UW	2	wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6Rep2	1x50		Alignments Unrestricted date: 2012-03-29	Alignments Unrestricted date: 2012-03-29
UW	1,2	wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6Rep1,wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6Rep2	1x50	.			ExonsEnsV65IAcuff Unrestricted date: None GeneEnsV65IAcuff Unrestricted date: None	TranscriptEnsV65IAcuff Unrestricted date: None

polyA

riboZeroGold

total

WholeBrain Strain: C57BL/6J Age: E14.5 Sex: U

2

WholeBrain, C57BL/6J, E14.5, U, RnaSeq (Gingeras), longPolyA, Whole-cell

Experiment				Data files
Lab	Biological Replicate	Internal Name	Read Type	bai	bam	bedRnaElements	bigWig	fastq	gtf	spikeins
CSHL	1	LID46987	2x101D	Alignments Unrestricted date: 2013-04-12	Alignments Unrestricted date: 2013-04-12		MinusRawSignal Unrestricted date: 2013-04-12 PlusRawSignal Unrestricted date: 2013-04-12	FastqRd1 Unrestricted date: 2013-04-12 FastqRd2 Unrestricted date: 2013-04-12		Spikeins Unrestricted date: 2013-05-01
CSHL	2	LID46988	2x101D	Alignments Unrestricted date: 2013-04-14	Alignments Unrestricted date: 2013-04-14		MinusRawSignal Unrestricted date: 2013-04-14 PlusRawSignal Unrestricted date: 2013-04-14	FastqRd1 Unrestricted date: 2013-04-14 FastqRd2 Unrestricted date: 2013-04-14		Spikeins Unrestricted date: 2013-05-01
CSHL	1,2	LID46987,LID46988	2x101D			Contigs Unrestricted date: 2013-04-13 Junctions Unrestricted date: 2013-04-13			ExonsDeNovo Unrestricted date: 2013-04-30 ExonsEnsV65IAcuff Unrestricted date: 2013-04-30 GeneDeNovo Unrestricted date: 2013-04-30 GeneEnsV65IAcuff Unrestricted date: 2013-04-30 TranscriptDeNovo Unrestricted date: 2013-04-30 TranscriptEnsV65IAcuff Unrestricted date: 2013-04-30

longPolyA

polyA

riboZeroGold

total

ENCODE RNA Dashboard (mm9)

Full list of data files & batch processing

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