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
  • 47ChIP-seq
Assay category
  • 47DNA binding
Target of assay
  • 47transcription factor
  • 14chromatin remodeller
  • 6RNA binding protein
  • 4recombinant protein
  • 2other post-translational modification
  • 1other context
Date released
  • 17July, 2011
  • 6August, 2012
  • 4March, 2012
  • 3December, 2016
  • 3February, 2012
  • 3June, 2011
  • 2April, 2012
  • 2October, 2011
  • 1December, 2014
  • 1July, 2014
  • 1July, 2016
  • 1June, 2016
  • 1March, 2014
  • 1September, 2011
  • 1September, 2012
Available data
  • 46bam
  • 46bigWig
  • 46fastq
  • 45bed narrowPeak
  • 45bigBed narrowPeak
  • 29bed broadPeak
  • 29bigBed broadPeak
  • 1bed bed9
  • 1bigBed bed9
Organism
  • 38Homo sapiens
  • 9Mus musculus
Biosample type
  • 39immortalized cell line
  • 4stem cell
  • 3tissue
  • 1primary cell
Organ
  • 1gonad
  • 1intestine
  • 1liver
  • 1small intestine
  • 1testis
Project
  • 47ENCODE
Genome assembly (visualization)
  • 35GRCh38
  • 19hg19
  • 9mm10
  • 7mm9
Audit category:
  • 1extremely low read length
Audit category:
  • 1415insufficient read depth
  • 838control insufficient read depth
  • 579missing controlled_by
  • 476insufficient read length
  • 310unreplicated experiment
  • 209poor library complexity
  • 202control low read depth
  • 197severe bottlenecking
  • 120insufficient spot score
  • 102partially characterized antibody
  • 82missing possible_controls
  • 66missing RNA fragment size
  • 47insufficient replicate concordance
  • 44missing documents
  • 20uncharacterized antibody
  • 17antibody not characterized to standard
  • 10missing spikeins
  • 2insufficient coverage
  • 2missing input control
Audit category:
  • 41low read length
  • 34low read depth
  • 31mild to moderate bottlenecking
  • 20moderate library complexity
  • 16control low read depth
  • 14inconsistent platforms
  • 9inconsistent control read length
  • 7mixed read lengths
  • 5inconsistent target of control experiment
  • 4mixed run types
  • 3inconsistent control run_type
BIOSAMPLE
ASSAY

47 results

search-icontable-tab-icon
Clear Filters
ChIP-seq
immortalized cell line
K56214
HepG25
CH12.LX3
GM128783
MCF-73
stem cell
H1-hESC4
tissue
liver1
small intestine1
testis1
primary cell
IMR-901
  • Contact
  • Terms of Use
  • Submitter sign-in

©2017 Stanford University.

  • ENCODE
  • UC Santa Cruz
  • Stanford University