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Experiment matrix

Enter search terms to filter the experiments included in the matrix.

Assay
  • shRNA RNA-seq
    440
  • Repli-chip
    63
  • CRISPR RNA-seq
    32
  • ChIP-seq
    13
  • DNase-seq
  • 5C
    9
  • FAIRE-seq
    9
  • total RNA-seq
    3
Assay category
  • Transcription
    475
  • Replication timing
    63
  • DNA binding
    13
  • 3D chromatin structure
    9
  • DNA accessibility
    9
Target of assay
  • RNA binding protein
    477
  • transcription factor
    100
Date released
  • August, 2015
    81
  • October, 2014
    72
  • December, 2014
    69
  • March, 2016
    65
  • November, 2014
    47
  • July, 2015
    36
  • September, 2016
    28
  • December, 2017
    23
  • January, 2016
    22
  • February, 2016
    21
  • July, 2012
    21
  • June, 2016
    21
  • March, 2011
    21
  • January, 2017
    20
  • October, 2011
    9
  • April, 2012
    6
  • August, 2016
    3
  • June, 2012
    3
  • August, 2012
    1
Available data
  • fastq
    13006
  • bam
    12177
  • bigWig
    11072
  • bigBed narrowPeak
    6662
  • bed narrowPeak
    6658
  • tsv
    2339
  • bed broadPeak
    1621
  • tagAlign
    1209
  • bigBed broadPeak
    1167
  • tar
    569
  • sra
    496
  • bed bedRnaElements
    288
  • bigBed bedRnaElements
    288
  • bed bedMethyl
    277
  • bigBed bedMethyl
    277
  • idat
    275
  • gtf
    269
  • bed tss_peak
    235
  • bigBed tss_peak
    235
  • gff gff3
    235
  • bed idr_peak
    134
  • bigBed idr_peak
    134
  • bed bed6+
    115
  • bigBed bed6+
    115
  • rcc
    115
  • bed bed3+
    91
  • bed bedLogR
    64
  • bigBed bedLogR
    63
  • sam
    59
  • wig
    59
  • bed bed12
    43
  • bigBed bed12
    43
  • bed bedGraph
    30
  • bed bedExonScore
    27
  • bigBed bedExonScore
    27
  • csfasta
    24
  • hdf5
    20
  • bed bed9
    18
  • bigBed bed9
    18
  • hic
    16
  • bigBed bed3+
    13
  • csqual
    12
  • vcf
    12
  • bed peptideMapping
    8
  • bigBed peptideMapping
    8
  • bed bed3
    7
  • bigBed bed3
    7
  • bed modPepMap
    6
  • bed pepMap
    6
  • bigBed modPepMap
    6
  • bigBed pepMap
    6
  • bedpe
    5
  • CEL
    4
  • fasta
    3
Experiment status
  • released
    569
Organism
  • Homo sapiens
    548
  • Mus musculus
    21
Biosample type
  • cell line
    524
  • in vitro differentiated cells
    35
  • primary cell
    10
Organ
  • blood
    255
  • bodily fluid
    255
  • liver
    245
  • embryo
    18
  • epithelium
    10
  • uterus
    5
  • skin of body
    4
  • connective tissue
    3
  • spleen
    3
  • blood vessel
    2
  • musculature of body
    2
  • vasculature
    2
  • vein
    2
  • brain
    1
  • intestine
    1
  • large intestine
    1
  • lung
    1
  • lymph node
    1
  • lymphoid tissue
    1
  • mammary gland
    1
  • penis
    1
  • prostate gland
    1
Cell
  • cancer cell
    492
  • epithelial cell
    252
  • stem cell
    20
  • lymphoblast
    12
  • hematopoietic cell
    6
  • myeloid cell
    4
  • B cell
    3
  • fibroblast
    3
  • myoblast
    3
  • endothelial cell
    2
  • induced pluripotent stem cell
    2
  • smooth muscle cell
    2
  • T cell
    1
  • keratinocyte
    1
  • leukocyte
    1
  • neural cell
    1
  • neuroblastoma cell
    1
Project
  • ENCODE
    569
Genome assembly
  • hg19
    547
  • GRCh38
    480
  • mm9
    21
  • mm10
    3
Lab
  • Brenton Graveley, UConn
    472
  • David Gilbert, FSU
    63
  • Vishwanath Iyer, UTA
    13
  • Jason Lieb, UNC
    9
  • John Stamatoyannopoulos, UW
    9
  • Michael Snyder, Stanford
    3
Audit category:
  • extremely low read depth
    3
  • inconsistent ontology term
    1
Audit category:
  • unreplicated experiment
    17
  • insufficient read length
    13
  • insufficient read depth
    7
  • poor library complexity
    1
  • severe bottlenecking
    1
Audit category:
  • missing analysis_step_run
    14
  • inconsistent platforms
    12
  • low read length
    4
  • mild to moderate bottlenecking
    4
  • inconsistent control read length
    2
  • low read depth
    2
  • moderate library complexity
    2
  • mixed read lengths
    1
assay_title!
  • DNase-seq
BIOSAMPLE
ASSAY

569 results

Clear Filters
shRNA RNA-seq
Repli-chip
CRISPR RNA-seq
ChIP-seq
5C
FAIRE-seq
total RNA-seq
cell line
HepG222314311
K56221718311
GM12878311
HeLa-S3131
MEL cell line12
in vitro differentiated cells
hepatocyte3
neural progenitor cell3
splanchnic mesodermal cell3
endodermal cell2
epiblast cell2
primary cell
myoblast3
endothelial cell of umbilical vein11
stem cell of epidermis2
T-cell1
embryonic fibroblast1
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