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Experiment matrix

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

Assay
  • ChIP-seq
    320
  • Repli-chip
    18
  • total RNA-seq
    3
  • MRE-seq
    2
  • MeDIP-seq
    2
Assay category
  • DNA binding
    320
  • Replication timing
    18
  • DNA methylation
    4
  • Transcription
    3
Target of assay
  • transcription factor
    153
  • histone
    112
  • broad histone mark
    60
  • control
    55
  • narrow histone mark
    49
  • chromatin remodeller
    23
  • other context
    3
  • other post-translational modification
    3
  • nucleotide modification
    2
  • RNA binding protein
    1
Date released
  • March, 2012
    52
  • August, 2012
    42
  • November, 2011
    41
  • September, 2011
    40
  • July, 2011
    28
  • June, 2011
    25
  • September, 2012
    22
  • April, 2012
    20
  • June, 2012
    19
  • July, 2012
    18
  • December, 2014
    14
  • February, 2014
    7
  • February, 2011
    5
  • March, 2014
    4
  • May, 2014
    4
  • February, 2012
    3
  • May, 2012
    1
Available data
  • bigWig
    341
  • bam
    327
  • fastq
    323
  • bed narrowPeak
    255
  • bigBed narrowPeak
    255
  • bed broadPeak
    132
  • bigBed broadPeak
    132
  • tar
    21
  • tsv
    3
  • fasta
    2
  • bed bed9
    1
  • bigBed bed9
    1
Experiment status
  • released
    345
Organism
  • Mus musculus
    345
Biosample type
  • cell line
    187
  • tissue
    111
  • in vitro differentiated cells
    34
  • primary cell
    13
Organ
  • spleen
    81
  • lymph node
    50
  • embryo
    44
  • musculature of body
    42
  • brain
    22
  • blood
    15
  • bodily fluid
    15
  • heart
    15
  • liver
    14
  • connective tissue
    11
  • bone element
    8
  • bone marrow
    8
  • gonad
    8
  • intestine
    8
  • kidney
    8
  • small intestine
    8
  • testis
    8
  • thymus
    8
  • lung
    5
  • adipose tissue
    4
  • extraembryonic component
    4
  • placenta
    4
  • epithelium
    2
  • skin of body
    2
  • limb
    1
Cell
  • cancer cell
    51
  • stem cell
    51
  • B cell
    50
  • fibroblast
    7
  • hematopoietic cell
    3
  • myeloid cell
    3
  • leukocyte
    1
  • lymphoblast
    1
  • neural cell
    1
Project
  • ENCODE
    345
Genome assembly
  • hg19
    9054
  • GRCh38
    8853
  • mm10
    1807
  • ce11
    950
  • dm6
    942
  • dm3
    932
  • ce10
    840
  • mm9
    345
  • GRCh38-minimal
    1
Lab
  • Bing Ren, UCSD
    142
  • Michael Snyder, Stanford
    111
  • Barbara Wold, Caltech
    42
  • Ross Hardison, PennState
    29
  • David Gilbert, FSU
    18
  • Sherman Weissman, Yale
    3
Audit category:
  • extremely low read depth
    22
Audit category:
  • insufficient read depth
    146
  • control insufficient read depth
    82
  • missing controlled_by
    58
  • insufficient read length
    32
  • poor library complexity
    21
  • severe bottlenecking
    14
  • insufficient replicate concordance
    7
  • missing documents
    4
Audit category:
  • low read length
    267
  • low read depth
    170
  • mild to moderate bottlenecking
    169
  • inconsistent platforms
    105
  • inconsistent target of control experiment
    80
  • control low read depth
    77
  • moderate library complexity
    76
  • inconsistent control read length
    32
  • borderline replicate concordance
    21
  • mixed read lengths
    21
organ_slims!
  • epithelium
BIOSAMPLE
ASSAY

345 results

Clear Filters
ChIP-seq
Repli-chip
total RNA-seq
MRE-seq
MeDIP-seq
cell line
MEL cell line681211
CH12.LX47111
C2C1216
G1E-ER413
ES-Bruce410
tissue
heart15
liver14
kidney8
small intestine8
spleen8
in vitro differentiated cells
myocyte26
epiblast cell2
ectodermal cell1
endodermal cell1
mesodermal cell1
primary cell
embryonic fibroblast61
stem cell of epidermis2
bone marrow macrophage1
erythroblast1
megakaryocyte1
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