This page provides a summary of transcriptome data production within the ENCODE project.

 

Please observe the guidelines of the "ENCODE Consortium Data Release Policy Summary" when using ENCODE data.

 

The number of experiments produced for each combination of cell line + compartment + RNA fraction + technology is reported in the colored cells.

Clicking on a cell will expand its content, which comprises links to the ENCODE DCC and to various processed data, when available.

Consult the expanded table to see the content of all table cells at once.

 

Full list of data files & batch processing

Please note that processed files based on pooled replicates do not fit in the table below. The full list of data files is available in this index file (see the parsing/download instructions), which should be used for batch file processing.

 

Documentation

When available, README files for each view are made available in this repository. The file naming format of the README files is: "README_{view}.{extension}"

 

Tier 1

Cell Lines Compartments RNA Fractions
Whole-cell

Nucleus


Nucleolus


Chromatin


Nucleoplasm

Cytoplasm


Polysomes
 
GM12878
2
GM12878, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
1
GM12878, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
UW 1  
2
GM12878, RNASeq (GINGERAS), Long PolyA+, Whole-cell
8
GM12878, RNASeq (MYERS), Long PolyA+, Whole-cell

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate Internal Name Read Type Insert Length   FASTQ BAM BED BIGBED BIGWIG   GFF GTF   GTF
CSHL 2 GM12878.rep2Il400R2x75WC+ 2x75 400      
CSHL 2 GM12878.rep2Il400R2x75WC+ 2x75 200      
CSHL 1 GM12878.rep1Il200R2x75WC+ 2x75 200      
CALTECH 1 1x75D ilNA      
CALTECH 2 1x75D ilNA      
CALTECH 1 2x75 200      
CALTECH 2 2x75 200      
CALTECH 2 2x75 400      
2
GM12878, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
1
GM12878, RNA PET, Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BED BIGWIG
GIS 1  
1
GM12878, Tiling Arrays, Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
GM12878, RNASeq (GINGERAS), Long PolyA+, Nucleus
2
GM12878, CAGE, Long PolyA+, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
1
GM12878, RNA PET, Long PolyA+, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BED BIGWIG
GIS 1  
1
GM12878, Tiling Arrays, Long PolyA+, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
3
GM12878, RNASeq (GINGERAS), Long PolyA+, Cytoplasm
Long PolyA+
2
GM12878, RNASeq (GINGERAS), Long PolyA-, Whole-cell
1
GM12878, CAGE, Long PolyA-, Nucleus

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
RIKEN 0      
1
GM12878, Tiling Arrays, Long PolyA-, Nucleus

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
GM12878, RNASeq (GINGERAS), Long PolyA-, Nucleus
1
GM12878, CAGE, Long PolyA-, Cytoplasm

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
RIKEN 0      
1
GM12878, Tiling Arrays, Long PolyA-, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
GM12878, RNASeq (GINGERAS), Long PolyA-, Cytoplasm
Long PolyA-
3
GM12878, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 101  
CSHL 1 1x36  
CSHL 2 1x36  
3
GM12878, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF   SHORTFRAGS
CSHL 112    
CSHL 1 1x36    
CSHL 2 1x36    
2
GM12878, RNASeq (GINGERAS), Short Total, Chromatin

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 3 1x101  
CSHL 4 1x101  
3
GM12878, RNASeq (GINGERAS), Short Total, Cytoplasm

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF   SHORTFRAGS
CSHL 108    
CSHL 1 1x36    
CSHL 2 1x36    
Short Total
1
GM12878, Tiling Arrays, Total Long, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
GM12878, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
CSHL 1  
CSHL 2  
1
GM12878, CAGE, Total Long, Nucleolus

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
RIKEN 0      
1
GM12878, Tiling Arrays, Total Long, Nucleolus

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
Total Long
 
H1-hESC
2
H1-hESC, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
1
H1-hESC, RNA PET, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BED BIGWIG
GIS 1  
3
H1-hESC, RNASeq (GINGERAS), Long PolyA+, Whole-cell
12
H1-hESC, RNASeq (MYERS), Long PolyA+, Whole-cell

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate Internal Name Read Type Insert Length   FASTQ BAM BED BIGBED BIGWIG   GFF GTF   GTF
CSHL 1 H1-hESC.rep1Il400R2x75WC+ 2x75 400      
CSHL 4 H1-hESC.rep4Il200R2x75WC+ 2x75 200      
CSHL 3 H1-hESC.rep3Il200R2x75WC+ 2x75 200      
CSHL 2 H1-hESC.rep2Il200R2x75WC+ 2x75 200      
CSHL 1 H1-hESC.rep1Il400R2x75WC+ 2x75 200      
CALTECH 1 1x75D ilNA      
CALTECH 2 1x75D ilNA      
CALTECH 1 2x75 200      
CALTECH 2 2x75 200      
CALTECH 3 2x75 200      
CALTECH 4 2x75 200      
CALTECH 1 2x75 400      
1
H1-hESC, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate Internal Name   FASTQ BAM BIGWIG
RIKEN 2 006N+  
1
H1-hESC, RNASeq (GINGERAS), Long PolyA+, Nucleus

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate Internal Name Read Type   FASTQ BAM BIGWIG PDF   GFF GTF   BEDRNAELEMENTS GFF GTF
CSHL 2 006N+ 2x76D      
  • Contigs
    Restricted until: 2012-11-9
1
H1-hESC, CAGE, Long PolyA+, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate Internal Name   FASTQ BAM BIGWIG
RIKEN 2 006C+  
1
H1-hESC, RNASeq (GINGERAS), Long PolyA+, Cytoplasm

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate Internal Name Read Type   FASTQ BAM BIGWIG PDF   GFF GTF   BEDRNAELEMENTS GFF GTF
CSHL 2 006C+ 2x76D      
  • Contigs
    Restricted until: 2012-11-9
Long PolyA+
1
H1-hESC, CAGE, Long PolyA-, Whole-cell

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
RIKEN 0      
2
H1-hESC, RNASeq (GINGERAS), Long PolyA-, Whole-cell
1
H1-hESC, RNASeq (GINGERAS), Long PolyA-, Nucleus

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate Internal Name Read Type   FASTQ BAM BIGWIG PDF   GFF GTF   BEDRNAELEMENTS GFF GTF
CSHL 2 006N- 2x76D      
  • Contigs
    Restricted until: 2012-11-9
1
H1-hESC, RNASeq (GINGERAS), Long PolyA-, Cytoplasm

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate Internal Name Read Type   FASTQ BAM BIGWIG PDF   GFF GTF   BEDRNAELEMENTS GFF GTF
CSHL 2 006C- 2x76D      
  • Contigs
    Restricted until: 2012-11-9
Long PolyA-
2
H1-hESC, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x36  
CSHL 2 1x36  
1
H1-hESC, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF   BEDRNAELEMENTS
CSHL 2 1x36    
1
H1-hESC, RNASeq (GINGERAS), Short Total, Cytoplasm

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG   BEDRNAELEMENTS
CSHL 2 1x36    
Short Total
 
K562
2
K562, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
2
K562, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
K562, RNASeq (GINGERAS), Long PolyA+, Whole-cell
6
K562, RNASeq (MYERS), Long PolyA+, Whole-cell

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Internal Name Read Type Insert Length   FASTQ BAM BIGBED BIGWIG   GTF
CSHL 1 K562.rep1Il200R2x75WC+ 2x75 200    
CSHL 2 K562.rep2Il200R2x75WC+ 2x75 200    
CALTECH 1 1x75D ilNA    
CALTECH 2 1x75D ilNA    
CALTECH 1 2x75 200    
CALTECH 2 2x75 200    
2
K562, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
1
K562, RNA PET, Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BED BIGWIG
GIS 1  
1
K562, Tiling Arrays, Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
K562, RNASeq (GINGERAS), Long PolyA+, Nucleus
3
K562, CAGE, Long PolyA+, Cytoplasm
1
K562, RNA PET, Long PolyA+, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BED BIGWIG
GIS 1  
1
K562, Tiling Arrays, Long PolyA+, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
4
1
K562, RNA PET, Long PolyA+, Polysomes

Experiment

Raw Results

Lab Biological Replicate Internal Name   FASTQ BAM BED BIGWIG
GIS 1 gen0153P+  
Long PolyA+
2
K562, RNASeq (GINGERAS), Long PolyA-, Whole-cell
1
K562, CAGE, Long PolyA-, Nucleus

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   BAM BIGWIG CSFASTA CSQUAL   GTF   BEDRNAELEMENTS
RIKEN 0      
1
K562, Tiling Arrays, Long PolyA-, Nucleus

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
K562, RNASeq (GINGERAS), Long PolyA-, Nucleus
1
K562, CAGE, Long PolyA-, Cytoplasm

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   BAM BIGWIG CSFASTA CSQUAL   GTF   BEDRNAELEMENTS
RIKEN 0      
1
K562, Tiling Arrays, Long PolyA-, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
K562, RNASeq (GINGERAS), Long PolyA-, Cytoplasm
1
K562, CAGE, Long PolyA-, Polysomes

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
RIKEN 0      
1
K562, Tiling Arrays, Long PolyA-, Polysomes

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
Long PolyA-
4
K562, RNASeq (SNYDER), PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM
YALE  
PolyA+
3
K562, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF   SHORTFRAGS
CSHL 130    
CSHL 1 1x36    
CSHL 2 1x36    
3
K562, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF   SHORTFRAGS
CSHL 151    
CSHL 1 1x36    
CSHL 2 1x36    
3
K562, RNASeq (GINGERAS), Short Total, Nucleolus

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG   SHORTFRAGS
CSHL 143    
CSHL 3 1x36    
CSHL 4 1x36    
3
K562, RNASeq (GINGERAS), Short Total, Chromatin

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG   SHORTFRAGS
CSHL 133    
CSHL 3 1x36    
CSHL 4 1x36    
3
K562, RNASeq (GINGERAS), Short Total, Nucleoplasm

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG   SHORTFRAGS
CSHL 146    
CSHL 3 1x36    
CSHL 4 1x36    
3
K562, RNASeq (GINGERAS), Short Total, Cytoplasm

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF   SHORTFRAGS
CSHL 142    
CSHL 1 1x36    
CSHL 2 1x36    
1
K562, RNASeq (GINGERAS), Short Total, Polysomes

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate   FASTQ BAM BIGWIG   SHORTFRAGS
CSHL 154    
Short Total
1
K562, Tiling Arrays, Total Long, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
K562, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
CSHL 1  
CSHL 2  
1
K562, CAGE, Total Long, Nucleolus

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
RIKEN 0      
1
K562, RNA PET, Total Long, Nucleolus

Experiment

Raw Results

Lab Biological Replicate Internal Name   FASTQ BAM BED BIGWIG
GIS 1 gen0145NLt  
1
K562, Tiling Arrays, Total Long, Nucleolus

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
K562, RNASeq (GINGERAS), Total Long, Nucleolus
1
K562, CAGE, Total Long, Chromatin

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
RIKEN 0      
1
K562, RNA PET, Total Long, Chromatin

Experiment

Raw Results

Lab Biological Replicate Internal Name   FASTQ BAM BED BIGWIG
GIS 1 gen0135CHt  
1
K562, Tiling Arrays, Total Long, Chromatin

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
K562, RNASeq (GINGERAS), Total Long, Chromatin
1
K562, CAGE, Total Long, Nucleoplasm

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
RIKEN 0      
1
K562, RNA PET, Total Long, Nucleoplasm

Experiment

Raw Results

Lab Biological Replicate Internal Name   FASTQ BAM BED BIGWIG
GIS 1 gen0148NPt  
1
K562, Tiling Arrays, Total Long, Nucleoplasm

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
AFFY  
2
K562, RNASeq (GINGERAS), Total Long, Nucleoplasm
Total Long

Tier 2

Whole-cell

Nucleus


Nucleolus


Chromatin


Nucleoplasm

Cytoplasm


Polysomes
 
A549
2
A549, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
2
A549, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
A549, RNASeq (GINGERAS), Long PolyA+, Whole-cell
2
A549, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 3 1x50  
RIKEN 4 1x50  
2
A549, RNASeq (GINGERAS), Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 2x101D  
CSHL 4 2x101D  
2
A549, CAGE, Long PolyA+, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 3 1x50  
RIKEN 4 1x50  
2
A549, RNASeq (GINGERAS), Long PolyA+, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 2x101D  
CSHL 4 2x101D  
Long PolyA+
2
A549, RNASeq (GINGERAS), Long PolyA-, Whole-cell
Long PolyA-
4
A549, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 1x101  
CSHL 4 1x101  
CSHL 1 1x101  
CSHL 2 1x101  
2
A549, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 1x101  
CSHL 4 1x101  
2
A549, RNASeq (GINGERAS), Short Total, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 1x101  
CSHL 4 1x101  
Short Total
 
HUVEC
2
HUVEC, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
2
HUVEC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
HUVEC, RNASeq (GINGERAS), Long PolyA+, Whole-cell
6
HUVEC, RNASeq (MYERS), Long PolyA+, Whole-cell

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Internal Name Read Type Insert Length   FASTQ BAM BIGBED BIGWIG   GTF
CSHL 2 HUVEC.rep2Il200R2x75WC+ 2x75 200    
CSHL 1 HUVEC.rep1Il200R2x75WC+ 2x75 200    
CALTECH 1 1x75D ilNA    
CALTECH 2 1x75D ilNA    
CALTECH 1 2x75 200    
CALTECH 2 2x75 200    
2
HUVEC, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 3  
RIKEN 4  
1
HUVEC, RNA PET, Long PolyA+, Nucleus

Experiment

Raw Results

Lab Biological Replicate Internal Name   FASTQ BAM BED BIGWIG
GIS 1 gen0118N+  
2
HUVEC, RNASeq (GINGERAS), Long PolyA+, Nucleus
2
HUVEC, CAGE, Long PolyA+, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 3  
RIKEN 4  
1
HUVEC, RNA PET, Long PolyA+, Cytoplasm

Experiment

Raw Results

Lab Biological Replicate Internal Name   FASTQ BAM BED BIGWIG
GIS 1 gen0117C+  
2
HUVEC, RNASeq (GINGERAS), Long PolyA+, Cytoplasm
Long PolyA+
2
HUVEC, RNASeq (GINGERAS), Long PolyA-, Whole-cell
1
HUVEC, CAGE, Long PolyA-, Nucleus

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x36  
2
HUVEC, RNASeq (GINGERAS), Long PolyA-, Nucleus
1
HUVEC, CAGE, Long PolyA-, Cytoplasm

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
RIKEN 0      
1
HUVEC, RNASeq (GINGERAS), Long PolyA-, Cytoplasm

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)

Lab Biological Replicate Internal Name Read Type   FASTQ BAM BIGWIG PDF   GFF GTF   BEDRNAELEMENTS GFF GTF
CSHL 3 029C- 2x76D      
  • Contigs
    Restricted until: 2012-11-9
Long PolyA-
2
HUVEC, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results

Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 1x36  
CSHL 4 1x36  
Short Total
 
HeLa-S3
2
HeLa-S3, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
2
HeLa-S3, RNA PET, Long PolyA+, Whole-cell
2
HeLa-S3, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results

Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
HeLa-S3, RNASeq (GINGERAS), Long PolyA+, Whole-cell
6
HeLa-S3, RNASeq (MYERS), Long PolyA+, Whole-cell

Experiment

Raw Results

Processed Results (Gencode agnostic)

Lab Biological Replicate Internal Name Read Type Insert Length   FASTQ BAM BIGBED BIGWIG   GTF
CSHL 2 HeLa-S3.rep2Il200R2x75WC+ 2x75 200    
CSHL 1 HeLa-S3.rep1Il200R2x75WC+ 2x75 200    
CALTECH 1 1x75D ilNA    
CALTECH 2 1x75D ilNA    
CALTECH 1 2x75 200    
CALTECH 2 2x75 200    
2