Go back to the ENCODE RNA Dashboard to see the overview of the table.

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
HeLa-S3, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
1
HeLa-S3, RNA PET, Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BED BIGWIG
GIS 1  
2
HeLa-S3, RNASeq (GINGERAS), Long PolyA+, Nucleus
2
HeLa-S3, CAGE, Long PolyA+, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
1
HeLa-S3, RNA PET, Long PolyA+, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BED BIGWIG
GIS 1  
2
HeLa-S3, RNASeq (GINGERAS), Long PolyA+, Cytoplasm
Long PolyA+
2
HeLa-S3, RNASeq (GINGERAS), Long PolyA-, Whole-cell
1
HeLa-S3, CAGE, Long PolyA-, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x36  
2
HeLa-S3, RNASeq (GINGERAS), Long PolyA-, Nucleus
1
HeLa-S3, 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
HeLa-S3, 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 GTF
CSHL 2 012C- 2x76D      
  • Contigs
    Restricted until: 2012-11-9
Long PolyA-
2
HeLa-S3, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x36  
CSHL 2 1x36  
2
HeLa-S3, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x36  
CSHL 2 1x36  
2
HeLa-S3, RNASeq (GINGERAS), Short Total, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x36  
CSHL 2 1x36  
Short Total
1
HeLa-S3, 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      
Total Long
 
HepG2
2
HepG2, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
2
HepG2, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
HepG2, RNASeq (GINGERAS), Long PolyA+, Whole-cell
6
HepG2, 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 HepG2.rep2Il200R2x75WC+ 2x75 200    
CSHL 1 HepG2.rep1Il200R2x75WC+ 2x75 200    
CALTECH 1 1x75D ilNA    
CALTECH 2 1x75D ilNA    
CALTECH 1 2x75 200    
CALTECH 2 2x75 200    
2
HepG2, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
1
HepG2, RNA PET, Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BED BIGWIG
GIS 1  
1
HepG2, Tiling Arrays, Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
AFFY  
2
HepG2, RNASeq (GINGERAS), Long PolyA+, Nucleus
2
HepG2, CAGE, Long PolyA+, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
1
HepG2, RNA PET, Long PolyA+, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BED BIGWIG
GIS 1  
1
HepG2, Tiling Arrays, Long PolyA+, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
AFFY  
2
HepG2, RNASeq (GINGERAS), Long PolyA+, Cytoplasm
Long PolyA+
2
HepG2, RNASeq (GINGERAS), Long PolyA-, Whole-cell
1
HepG2, 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
HepG2, Tiling Arrays, Long PolyA-, Nucleus

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
AFFY  
2
HepG2, RNASeq (GINGERAS), Long PolyA-, Nucleus
1
HepG2, 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
HepG2, Tiling Arrays, Long PolyA-, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
AFFY  
2
HepG2, RNASeq (GINGERAS), Long PolyA-, Cytoplasm
Long PolyA-
2
HepG2, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x36  
CSHL 2 1x36  
2
HepG2, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x36  
CSHL 2 1x36  
2
HepG2, RNASeq (GINGERAS), Short Total, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x36  
CSHL 2 1x36  
Short Total
1
HepG2, 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
HepG2, Tiling Arrays, Total Long, Nucleolus

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
AFFY  
Total Long
 
IMR90
2
IMR90, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
2
IMR90, RNASeq (GINGERAS), Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 2x101D  
CSHL 2 2x101D  
2
IMR90, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
2
IMR90, RNASeq (GINGERAS), Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 2x101D  
CSHL 2 2x101D  
2
IMR90, CAGE, Long PolyA+, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
2
IMR90, RNASeq (GINGERAS), Long PolyA+, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 2x101D  
CSHL 2 2x101D  
Long PolyA+
2
IMR90, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x101  
CSHL 2 1x101  
2
IMR90, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x101  
CSHL 2 1x101  
2
IMR90, RNASeq (GINGERAS), Short Total, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
IMR90, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 2x101D  
CSHL 2 2x101D  
Total Long
 
MCF-7
2
MCF-7, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
2
MCF-7, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
MCF-7, RNASeq (GINGERAS), Long PolyA+, Whole-cell
5
2
MCF-7, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 3 1x50  
RIKEN 4 1x50  
2
MCF-7, RNASeq (GINGERAS), Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 2x101D  
CSHL 4 2x101D  
2
MCF-7, CAGE, Long PolyA+, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 3 1x50  
RIKEN 4 1x50  
2
MCF-7, 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
MCF-7, RNASeq (GINGERAS), Long PolyA-, Whole-cell
Long PolyA-
4
MCF-7, 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
MCF-7, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 1x101  
CSHL 4 1x101  
2
MCF-7, 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
 
Monocytes-CD14+
2
Monocytes-CD14+, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
2
Monocytes-CD14+, RNASeq (GINGERAS), Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 2x76D  
CSHL 2 2x76D  
Long PolyA+
2
Monocytes-CD14+, RNASeq (GINGERAS), Long PolyA-, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 2x76D  
CSHL 2 2x76D  
Long PolyA-
2
Monocytes-CD14+, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x36  
CSHL 2 1x36  
Short Total
 
SK-N-SH
2
SK-N-SH, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 3 1x50  
RIKEN 4 1x50  
2
SK-N-SH, RNASeq (GINGERAS), Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 2x101D  
CSHL 4 2x101D  
2
SK-N-SH, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 3 1x50  
RIKEN 4 1x50  
2
SK-N-SH, RNASeq (GINGERAS), Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 2x101D  
CSHL 4 2x101D  
2
SK-N-SH, CAGE, Long PolyA+, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 3 1x50  
RIKEN 4 1x50  
2
SK-N-SH, 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
SK-N-SH, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 1x101  
CSHL 4 1x101  
2
SK-N-SH, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 1x101  
CSHL 4 1x101  
2
SK-N-SH, RNASeq (GINGERAS), Short Total, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 3 1x101  
CSHL 4 1x101  
Short Total

Tier 3

Whole-cell

Nucleus


Nucleolus


Chromatin


Nucleoplasm

Cytoplasm


Polysomes
 
AG04449
2
AG04449, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
AG04450
2
AG04450, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
2
AG04450, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
AG04450, RNASeq (GINGERAS), Long PolyA+, Whole-cell
Long PolyA+
2
AG04450, RNASeq (GINGERAS), Long PolyA-, Whole-cell
Long PolyA-
2
AG04450, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x36  
CSHL 2 1x36  
Short Total
 
AG09309
2
AG09309, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
AG09319
2
AG09319, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
AG10803
2
AG10803, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
AoAF
2
AoAF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
BE2_C
2
BE2_C, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
BJ
2
BJ, CAGE, Long PolyA+, Whole-cell

Experiment

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

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
BJ, RNASeq (GINGERAS), Long PolyA+, Whole-cell
Long PolyA+
2
BJ, RNASeq (GINGERAS), Long PolyA-, Whole-cell
Long PolyA-
2
BJ, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x36  
CSHL 2 1x36  
Short Total
 
CD20+
2
CD20+, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
2
CD20+, RNASeq (GINGERAS), Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 2x76D  
CSHL 2 2x76D  
Long PolyA+
2
CD20+, RNASeq (GINGERAS), Long PolyA-, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 2x76D  
CSHL 2 2x76D  
Long PolyA-
2
CD20+, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 2 1x36  
CSHL 1 1x36  
Short Total
 
CD34+_Mobilized
1
CD34+_Mobilized, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results

Processed Results (Gencode agnostic)
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG   BEDRNAELEMENTS
RIKEN 1 1x50    
Long PolyA+
1
CD34+_Mobilized, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
CSHL 1 1x101      
  • Contigs
    Restricted until: 2013-1-21
Short Total
1
CD34+_Mobilized, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)
Lab Biological Replicate Internal Name Read Type   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS GFF GTF
CSHL 1 043WCt 2x101D      
  • Contigs
    Restricted until: 2012-12-14
Total Long
 
CMK
1
CMK, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
Long PolyA+
 
Caco-2
2
Caco-2, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
GM06990
2
GM06990, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
GM12864
1
GM12864, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
Long PolyA+
 
GM12865
2
GM12865, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
GM12891
4
GM12891, 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 GM12891.rep2Il200R2x75WC+ 2x75 200    
CSHL 1 GM12891.rep1Il200R2x75WC+ 2x75 200    
CALTECH 1 2x75 200    
CALTECH 2 2x75 200    
Long PolyA+
 
GM12892
6
GM12892, 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 GM12892.rep2Il200R2x75WC+ 2x75 200      
CSHL 1 GM12892.rep1Il200R2x75WC+ 2x75 200      
CSHL 3 GM12892.rep3Il200R2x75WC+ 2x75 200  
  • Contigs
    Restricted until: To be decided
   
CALTECH 1 2x75 200      
CALTECH 2 2x75 200      
CALTECH 3 2x75 200      
Long PolyA+
 
H7-hESC
2
H7-hESC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HA-h
2
HA-h, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HA-sp
2
HA-sp, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HAEpiC
2
HAEpiC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HAc
2
HAc, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HAoAF
2
HAoAF, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
HAoAF, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 2 1x101  
CSHL 1 1x101  
Short Total
1
HAoAF, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)
Lab Biological Replicate Internal Name Read Type   FASTQ BAM BIGWIG PDF   GTF   GFF GTF
CSHL 2 056WCt 2x101D      
Total Long
 
HAoEC
2
HAoEC, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
HAoEC, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
HAoEC, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 2x101D  
CSHL 2 2x101D  
Total Long
 
HBMEC
2
HBMEC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HBVP
1
HBVP, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
Long PolyA+
 
HBVSMC
2
HBVSMC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HCF
2
HCF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HCFaa
2
HCFaa, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HCH
2
HCH, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
HCH, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
HCH, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 2x101D  
CSHL 2 2x101D  
Total Long
 
HCM
2
HCM, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HCPEpiC
2
HCPEpiC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HCT-116
2
HCT-116, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
4
HCT-116, 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 HCT-116.rep1Il200R2x75WC+ 2x75 200    
CSHL 2 HCT-116.rep2Il200R2x75WC+ 2x75 200    
CALTECH 1 2x75 200    
CALTECH 2 2x75 200    
Long PolyA+
 
HConF
2
HConF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HEEpiC
2
HEEpiC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HEK293
2
HEK293, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HFDPC
2
HFDPC, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
HFDPC, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 2 1x101  
CSHL 1 1x101  
Short Total
2
HFDPC, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 2 2x101D  
CSHL 1 2x101D  
Total Long
 
HFF
2
HFF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HFF-Myc
2
HFF-Myc, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HGF
2
HGF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HIPEpiC
2
HIPEpiC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HL-60
2
HL-60, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HMEC
2
HMEC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
1
HMEC, RNASeq (GINGERAS), Long PolyA+, Whole-cell

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 1 036WC+ 2x76D      
  • Contigs
    Restricted until: 2012-11-9
Long PolyA+
1
HMEC, RNASeq (GINGERAS), Long PolyA-, Whole-cell

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 1 036WC- 2x76D      
  • Contigs
    Restricted until: 2012-11-9
Long PolyA-
 
HMEpC
1
HMEpC, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results

Processed Results (Gencode agnostic)
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG   BEDRNAELEMENTS
RIKEN 1 1x50    
Long PolyA+
1
HMEpC, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
CSHL 1 1x101      
  • Contigs
    Restricted until: 2013-1-21
Short Total
1
HMEpC, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)
Lab Biological Replicate Internal Name Read Type   FASTQ BAM BIGWIG PDF   GTF   BEDRNAELEMENTS GFF GTF
CSHL 1 . 2x101D      
  • Contigs
    Restricted until: 2012-12-14
Total Long
 
HMF
2
HMF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HMVEC-LBl
2
HMVEC-LBl, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HMVEC-LLy
2
HMVEC-LLy, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HMVEC-dAd
2
HMVEC-dAd, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HMVEC-dBl-Ad
2
HMVEC-dBl-Ad, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HMVEC-dBl-Neo
2
HMVEC-dBl-Neo, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HMVEC-dLy-Ad
2
HMVEC-dLy-Ad, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HMVEC-dLy-Neo
2
HMVEC-dLy-Neo, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HMVEC-dNeo
2
HMVEC-dNeo, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HNPCEpiC
2
HNPCEpiC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HOB
2
HOB, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
1
HOB, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
CSHL 2 1x101      
  • Contigs
    Restricted until: 2013-1-21
Short Total
2
HOB, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 2 2x101D  
CSHL 1 2x101D  
Total Long
 
HPAEC
1
HPAEC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
Long PolyA+
 
HPAF
2
HPAF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HPC-PL
2
HPC-PL, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
HPC-PL, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
HPC-PL, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 2x101D  
CSHL 2 2x101D  
Total Long
 
HPF
2
HPF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HPIEpC
2
HPIEpC, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
HPIEpC, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
HPIEpC, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 2x101D  
CSHL 2 2x101D  
Total Long
 
HPdLF
2
HPdLF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HRCEpiC
2
HRCEpiC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HRE
2
HRE, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HRGEC
2
HRGEC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HRPEpiC
2
HRPEpiC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HSMM
2
HSMM, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
HSMM, RNASeq (GINGERAS), Long PolyA+, Whole-cell
4
HSMM, 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 HSMM.rep2Il200R2x75WC+ 2x75 200    
CSHL 1 HSMM.rep1Il200R2x75WC+ 2x75 200    
CALTECH 1 2x75 200    
CALTECH 2 2x75 200    
Long PolyA+
2
HSMM, RNASeq (GINGERAS), Long PolyA-, Whole-cell
Long PolyA-
 
HSMMtube
2
HSMMtube, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
HSaVEC
2
HSaVEC, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
HSaVEC, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
HSaVEC, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 2x101D  
CSHL 2 2x101D  
Total Long
 
HVMF
2
HVMF, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
2
HVMF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
2
HVMF, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
HVMF, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 2x101D  
CSHL 2 2x101D  
Total Long
 
HWP
2
HWP, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
HWP, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
HWP, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 2 2x101D  
CSHL 1 2x101D  
Total Long
 
Jurkat
2
Jurkat, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
LHCN-M2
2
Long PolyA+
 
LNCaP
2
LNCaP, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
NB4
2
NB4, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
NH-A
2
NH-A, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
NHBE
2
NHBE, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
NHDF
2
NHDF, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
NHDF, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 2 1x101  
CSHL 1 1x101  
Short Total
2
NHDF, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 2 2x101D  
CSHL 1 2x101D  
Total Long
 
NHDF-Ad
2
NHDF-Ad, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
NHDF-neo
2
NHDF-neo, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
NHEK
2
NHEK, CAGE, Long PolyA+, Whole-cell

Experiment

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

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
3
NHEK, RNASeq (GINGERAS), Long PolyA+, Whole-cell

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 5 035WC+ 2x76D      
  • Contigs
    Restricted until: 2012-11-9
CSHL 1 2x76D      
CSHL 2 2x76D      
5
NHEK, 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 NHEK.rep1Il200R2x75WC+ 2x75 200    
CSHL 2 NHEK.rep2Il200R2x75WC+ 2x75 200    
CALTECH 1 1x75D ilNA    
CALTECH 1 2x75 200    
CALTECH 2 2x75 200    
2
NHEK, CAGE, Long PolyA+, Nucleus

Experiment

Raw Results

Processed Results (Gencode dependent)

Processed Results (Gencode agnostic)
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG   GTF   BEDRNAELEMENTS
RIKEN 3      
RIKEN 4 1x36      
1
NHEK, RNA PET, Long PolyA+, Nucleus

Experiment

Raw Results
Lab Biological Replicate Internal Name   FASTQ BAM BED BIGWIG
GIS 1 gen0158N+  
1
NHEK, Tiling Arrays, Long PolyA+, Nucleus

Experiment

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

Experiment

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

Experiment

Raw Results
Lab Biological Replicate Internal Name   FASTQ BAM BED BIGWIG
GIS 1 gen0156C+  
1
NHEK, Tiling Arrays, Long PolyA+, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
AFFY  
2
NHEK, RNASeq (GINGERAS), Long PolyA+, Cytoplasm
Long PolyA+
3
NHEK, RNASeq (GINGERAS), Long PolyA-, Whole-cell

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 5 035WC- 2x76D      
  • Contigs
    Restricted until: 2012-11-9
CSHL 1 2x76D      
CSHL 2 2x76D      
1
NHEK, 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
NHEK, Tiling Arrays, Long PolyA-, Nucleus

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
AFFY  
2
NHEK, RNASeq (GINGERAS), Long PolyA-, Nucleus
1
NHEK, 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
NHEK, Tiling Arrays, Long PolyA-, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
AFFY  
1
NHEK, 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   GFF GTF   BEDRNAELEMENTS GFF GTF
CSHL 3 027C- 2x76D      
  • Contigs
    Restricted until: 2012-11-9
Long PolyA-
2
NHEK, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x36  
CSHL 2 1x36  
2
NHEK, RNASeq (GINGERAS), Short Total, Nucleus

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 1x36  
CSHL 4 1x36  
2
NHEK, RNASeq (GINGERAS), Short Total, Cytoplasm

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 3 1x36  
CSHL 4 1x36  
Short Total
 
NHEM.f_M2
2
NHEM.f_M2, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
NHEM.f_M2, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
NHEM.f_M2, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 2 2x101D  
CSHL 1 2x101D  
Total Long
 
NHEM_M2
2
NHEM_M2, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
NHEM_M2, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
NHEM_M2, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 2 2x101D  
CSHL 1 2x101D  
Total Long
 
NHLF
2
NHLF, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
NHLF, RNASeq (GINGERAS), Long PolyA+, Whole-cell
4
NHLF, 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 NHLF.rep2Il200R2x75WC+ 2x75 200    
CSHL 1 NHLF.rep1Il200R2x75WC+ 2x75 200    
CALTECH 1 2x75 200    
CALTECH 2 2x75 200    
Long PolyA+
2
NHLF, RNASeq (GINGERAS), Long PolyA-, Whole-cell
Long PolyA-
 
NT2-D1
2
NT2-D1, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
PANC-1
2
PANC-1, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
PrEC
2
PrEC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
RPTEC
2
RPTEC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
SAEC
2
SAEC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
SK-N-MC
2
SK-N-MC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
SK-N-SH_RA
2
SK-N-SH_RA, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   FASTQ BAM BIGWIG
RIKEN 1  
RIKEN 2  
2
SK-N-SH_RA, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
2
SK-N-SH_RA, RNASeq (GINGERAS), Long PolyA+, Whole-cell
Long PolyA+
2
SK-N-SH_RA, RNASeq (GINGERAS), Long PolyA-, Whole-cell
Long PolyA-
2
SK-N-SH_RA, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 1x36  
CSHL 2 1x36  
Short Total
 
SkMC
2
SkMC, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
2
SkMC, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
2
SkMC, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 2 1x101  
CSHL 1 1x101  
Short Total
2
SkMC, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 2 2x101D  
CSHL 1 2x101D  
Total Long
 
Th1
1
Th1, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
Long PolyA+
 
WERI-Rb-1
1
WERI-Rb-1, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
Long PolyA+
 
WI-38
4
WI-38, Exon Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
UW 1  
UW 2  
Long PolyA+
 
hMNC-CB
1
hMNC-CB, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results

Processed Results (Gencode agnostic)
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF   BEDRNAELEMENTS
CSHL 2 2x101D    
  • Contigs
    Restricted until: 2012-12-28
Total Long
 
hMNC-PB
1
hMNC-PB, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results

Processed Results (Gencode agnostic)
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF   BEDRNAELEMENTS
CSHL 1 2x101D    
  • Contigs
    Restricted until: 2012-12-28
Total Long
 
hMSC-AT
2
hMSC-AT, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
hMSC-AT, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
hMSC-AT, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 1 2x101D  
CSHL 2 2x101D  
Total Long
 
hMSC-BM
2
hMSC-BM, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
hMSC-BM, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG PDF
CSHL 2 2x101D  
CSHL 1 2x101D  
Total Long
 
hMSC-UC
2
hMSC-UC, CAGE, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
RIKEN 1 1x50  
RIKEN 2 1x50  
Long PolyA+
2
hMSC-UC, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 1x101  
CSHL 2 1x101  
Short Total
2
hMSC-UC, RNASeq (GINGERAS), Total Long, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Read Type   FASTQ BAM BIGWIG
CSHL 1 2x101D  
CSHL 2 2x101D  
Total Long
 
prostate
1
prostate, RNA PET, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate Internal Name   FASTQ BAM BED BIGWIG
GIS 1 gen0160WC+  
1
prostate, Tiling Arrays, Long PolyA+, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
AFFY  
Long PolyA+
1
prostate, CAGE, Long PolyA-, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BAM BIGWIG CSFASTA CSQUAL
RIKEN 0  
1
prostate, Tiling Arrays, Long PolyA-, Whole-cell

Experiment

Raw Results
Lab Biological Replicate   BROADPEAK
AFFY  
Long PolyA-
1
prostate, RNASeq (GINGERAS), Short Total, Whole-cell

Experiment

Raw Results

Processed Results (Gencode agnostic)
Lab Biological Replicate   FASTQ BAM BIGWIG   SHORTFRAGS
CSHL 161    
Short Total

Technologies

CAGE

Cap analysis gene expression (CAGE) is a technique used to produce a snapshot of the 5' end of the messenger RNA population in a biological sample. The small fragments from the very beginnings of mRNAs (5' ends of capped transcripts) are extracted, reverse-transcribed to DNA, PCR amplified and sequenced. More...

RNA PET

RNA PET analysis targets 5' and 3' ends of mRNAs, which are subsequently sequenced and mapped to the genome. It permits the precise delimitation of transcription start and termination sites. More...

Tiling Arrays

Microarray hybridization data obtained using the Affymetrix Whole-Genome Tiling Arrays. More...

Exon Arrays

Microarray hybridization data obtained using the Affymetrix Human Exon 1.0 GeneChip. In contrast to traditional microarrays, which are designed to measure overall gene expression, the Affymetrix exon arrays contain separate probesets for each exon. This allows large-scale measurement of alternative splicing, alternative polyadenylation, and alternative promoter usage. Additionally, analysis of the constitutive exons (those included in all transcripts) offer accurate measurement of overall gene expression levels. More...

RNASeq (GINGERAS)
RNASeq (SNYDER)
RNASeq (MYERS)

RNA sequencing, or RNA-seq, is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly. RNA-seq is performed by reverse-transcribing an RNA sample into cDNA followed by high throughput DNA sequencing. More...

Cell Lines

The UCSC has further information on the cell lines: Further Info

Compartments

Whole-cell

Whole cell
Nucleus

Large membrane bound part of cell containing chromosomes and the bulk of the DNA
Nucleolus

The part of the nucleus where ribosomal RNA is actively transcribed
Chromatin

Nuclear DNA and associated proteins
Nucleoplasm

That part of the nuclear content other than the chromosomes or the nucleolus
Cytoplasm

The fluid between the cells outer membrane and the nucleus
Polysomes

Strand of mRNA with ribosomes attached

RNA Fractions

Long PolyA+

Poly(A)+ RNA longer than 200 nt
Long PolyA-

Poly(A)- RNA longer than 200 nt
PolyA+

Poly(A)+ RNA
Short Total

RNA shorter than 200 nt, not Poly(A)-separated
Total Long

RNA longer than 200 nt, not Poly(A)-separated