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

Experiment Matrix

Click or enter search terms to filter the experiments included in the matrix.

Assay
  • 1090ChIP-seq
Assay category
  • 1090DNA binding
Target of assay
  • 517histone
  • 517histone modification
  • 504transcription factor
  • 263narrow histone mark
  • 216broad histone mark
  • 148RNA binding protein
  • 64control
  • 57chromatin remodeller
  • 52recombinant protein
  • 10other post-translational modification
  • 6other context
Date released
  • 189July, 2013
  • 83July, 2011
  • 57January, 2017
  • 57June, 2014
  • 53July, 2014
  • 48August, 2012
  • 43February, 2011
  • 43November, 2016
  • 38March, 2012
  • 38May, 2016
  • 37October, 2016
  • 32July, 2016
  • 29March, 2011
  • 26December, 2016
  • 25September, 2012
  • 24February, 2012
  • 23March, 2016
  • 22June, 2017
  • 21February, 2017
  • 21October, 2011
  • 18March, 2017
  • 17June, 2015
  • 15April, 2012
  • 14September, 2016
  • 12November, 2011
  • 11December, 2014
  • 10June, 2016
  • 10May, 2012
  • 9April, 2017
  • 8April, 2016
  • 8January, 2012
  • 8November, 2015
  • 7June, 2012
  • 6September, 2011
  • 5August, 2016
  • 5September, 2014
  • 4August, 2015
  • 4February, 2016
  • 3May, 2017
  • 2January, 2016
  • 2June, 2011
  • 1May, 2011
  • 1November, 2014
  • 1October, 2014
Available data
  • 1085fastq
  • 1055bam
  • 922bigWig
  • 898bed narrowPeak
  • 894bigBed narrowPeak
  • 350bed broadPeak
  • 279bigBed broadPeak
  • 169tagAlign
  • 2tar
Organism
  • 831Homo sapiens
  • 225Mus musculus
  • 21Caenorhabditis elegans
  • 13Drosophila melanogaster
Biosample type
  • 412immortalized cell line
  • 368tissue
  • 115primary cell
  • 105in vitro differentiated cells
  • 44stem cell
  • 34whole organisms
  • 12induced pluripotent stem cell line
Organ
  • 60brain
  • 42embryonic structure
  • 40heart
  • 34connective tissue
  • 33muscle organ
  • 32liver
  • 30intestine
  • 25blood vessel
  • 25skin of body
  • 21esophagus
  • 17stomach
  • 16extraembryonic component
  • 14large intestine
  • 11adrenal gland
  • 11gonad
  • 10adipose tissue
  • 9kidney
  • 9lung
  • 8small intestine
  • 8thymus
  • 8vein
  • 7breast
  • 7spleen
  • 7vagina
  • 6pancreas
  • 6testis
  • 6thyroid gland
  • 5artery
  • 5ovary
  • 5prostate gland
  • 3bone element
  • 3urinary bladder
  • 2mouth
  • 2penis
  • 2uterus
  • 1bronchus
  • 1eye
  • 1mammary gland
  • 1placenta
  • 1spinal cord
Project
  • 867ENCODE
  • 189Roadmap
  • 34modERN
Genome assembly (visualization)
  • 583GRCh38
  • 510hg19
  • 218mm10
  • 80mm9
  • 21ce10
  • 21ce11
  • 13dm3
  • 13dm6
Audit category:
  • 19extremely low read depth
  • 14control extremely low read depth
  • 4extremely low read length
Audit category:
  • 359insufficient read depth
  • 150control insufficient read depth
  • 98missing controlled_by
  • 81severe bottlenecking
  • 61poor library complexity
  • 60control low read depth
  • 20insufficient read length
  • 20insufficient replicate concordance
  • 19partially characterized antibody
  • 7missing possible_controls
  • 4antibody not characterized to standard
  • 4uncharacterized antibody
  • 1missing documents
  • 1unreplicated experiment
Audit category:
  • 2854low read length
  • 2426mild to moderate bottlenecking
  • 1814low read depth
  • 1090moderate library complexity
  • 967inconsistent platforms
  • 849inconsistent control read length
  • 736control low read depth
  • 568antibody characterized with exemption
  • 475mixed read lengths
  • 382insufficient read depth
  • 332borderline replicate concordance
  • 306missing external identifiers
  • 241inconsistent target of control experiment
  • 165low spot score
  • 149mixed run types
  • 133inconsistent control run_type
  • 110missing spikeins
  • 89low replicate concordance
  • 89missing genotype
  • 9missing tag construct
  • 1high lambda C methylation ratio
BIOSAMPLE
ASSAY

1090 results

search-icontable-tab-icon
Clear Filters
ChIP-seq
immortalized cell line
K562107
GM1287847
HepG230
MCF-728
MEL cell line24
tissue
liver29
heart20
hindbrain18
limb18
midbrain15
primary cell
common myeloid progenitor, CD34-positive13
CD4-positive helper T cell9
IMR-909
endothelial cell of umbilical vein8
B cell7
in vitro differentiated cells
trophoblast cell15
mesenchymal stem cell14
neural cell14
neuronal stem cell11
HUES64-derived CD184+7
stem cell
H1-hESC25
H98
ES-E143
ES-Bruce42
ES-I32
whole organisms
whole organism34
induced pluripotent stem cell line
iPS-18c4
induced pluripotent stem cell3
iPS DF 19.112
iPS-20b2
iPS-18a1
  • Contact
  • Terms of Use
  • Submitter sign-in

©2017 Stanford University.

  • ENCODE
  • UC Santa Cruz
  • Stanford University