ENCODE
    • Matrix
    • Search
    • Summary
    • Search by region
    • Reference epigenomes
    • Publications
    • About
    • Visualize (SCREEN)
    • Matrix
    • Search
    • Methods
    • Antibodies
    • Biosamples
    • Genome references
    • Standards and guidelines
    • Ontologies
    • File formats
    • Software tools
    • Pipelines
    • Release policy
    • Data access
    • Schemas
    • Getting started
    • Tutorials
    • REST API
    • Cart
    • Project overview
    • Acknowledgements
    • Contact
    • News
    • Citing ENCODE

Experiment matrix

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

Assay
  • ChIP-seq
    295
  • Repli-chip
    18
  • total RNA-seq
    3
  • MRE-seq
    2
  • MeDIP-seq
    2
Assay category
  • DNA binding
    295
  • Replication timing
    18
  • DNA methylation
    4
  • Transcription
    3
Target of assay
  • transcription factor
    153
  • histone
    92
  • broad histone mark
    50
  • control
    50
  • narrow histone mark
    39
  • 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
  • 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
    316
  • bam
    302
  • fastq
    298
  • bed narrowPeak
    235
  • bigBed narrowPeak
    235
  • bed broadPeak
    113
  • bigBed broadPeak
    113
  • tar
    21
  • tsv
    3
  • bed bed9
    1
  • bigBed bed9
    1
  • fasta
    1
Experiment status
  • released
    320
Organism
  • Mus musculus
    320
Biosample type
  • cell line
    184
  • tissue
    92
  • in vitro differentiated cells
    34
  • primary cell
    10
Organ
  • spleen
    79
  • lymph node
    50
  • musculature of body
    42
  • embryo
    38
  • brain
    16
  • blood
    15
  • bodily fluid
    15
  • heart
    12
  • liver
    12
  • connective tissue
    8
  • gonad
    8
  • intestine
    8
  • small intestine
    8
  • testis
    8
  • thymus
    8
  • bone element
    6
  • bone marrow
    6
  • kidney
    6
  • adipose tissue
    4
  • extraembryonic component
    4
  • placenta
    4
  • lung
    3
  • epithelium
    2
  • skin of body
    2
  • limb
    1
Cell
  • cancer cell
    51
  • B cell
    50
  • stem cell
    48
  • fibroblast
    4
  • hematopoietic cell
    3
  • myeloid cell
    3
  • leukocyte
    1
  • lymphoblast
    1
  • neural cell
    1
Project
  • ENCODE
    320
Genome assembly
  • hg19
    9036
  • GRCh38
    8840
  • mm10
    1782
  • ce11
    950
  • dm6
    942
  • dm3
    932
  • ce10
    840
  • mm9
    320
  • GRCh38-minimal
    1
Lab
  • Bing Ren, UCSD
    117
  • 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
    19
Audit category:
  • insufficient read depth
    125
  • control insufficient read depth
    71
  • missing controlled_by
    56
  • insufficient read length
    30
  • poor library complexity
    21
  • severe bottlenecking
    14
  • insufficient replicate concordance
    7
  • missing documents
    4
Audit category:
  • low read length
    244
  • mild to moderate bottlenecking
    160
  • low read depth
    159
  • inconsistent platforms
    103
  • inconsistent target of control experiment
    80
  • moderate library complexity
    75
  • control low read depth
    69
  • inconsistent control read length
    30
  • borderline replicate concordance
    21
  • mixed read lengths
    21
month_released!
  • June, 2011
BIOSAMPLE
ASSAY

320 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-E1491
tissue
heart12
liver12
small intestine8
testis8
thymus8
in vitro differentiated cells
myocyte26
epiblast cell2
ectodermal cell1
endodermal cell1
mesodermal cell1
primary cell
embryonic fibroblast31
stem cell of epidermis2
bone marrow macrophage1
erythroblast1
megakaryocyte1
  • Citing ENCODE
  • Privacy
  • Contact
  • Submitter sign-in
  • ENCODE
  • Stanford University

©2019 Stanford University