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
  • 859ChIP-seq
  • 30polyA mRNA RNA-seq
  • 28CAGE
  • 9Repli-chip
  • 8ATAC-seq
  • 8WGBS
  • 1genotyping HTS
  • 1microRNA-seq
  • 1total RNA-seq
Assay category
  • 859DNA binding
  • 60Transcription
  • 9Replication timing
  • 8DNA accessibility
  • 8DNA methylation
  • 8DNA sequencing
  • 1Genotyping
Target of assay
  • 518histone
  • 518histone modification
  • 303transcription factor
  • 246broad histone mark
  • 213narrow histone mark
  • 78RNA binding protein
  • 57chromatin remodeller
  • 36control
  • 13recombinant protein
  • 5other context
  • 5other post-translational modification
Date released
  • 165July, 2013
  • 96November, 2015
  • 80March, 2012
  • 76August, 2012
  • 64February, 2011
  • 56June, 2015
  • 47February, 2012
  • 47March, 2014
  • 37March, 2011
  • 36April, 2012
  • 32October, 2011
  • 28September, 2012
  • 21July, 2014
  • 20March, 2016
  • 19September, 2011
  • 14December, 2014
  • 14July, 2011
  • 14June, 2012
  • 13November, 2016
  • 11February, 2016
  • 10January, 2017
  • 9July, 2015
  • 7January, 2012
  • 7October, 2016
  • 5May, 2012
  • 4March, 2017
  • 2June, 2011
  • 2June, 2014
  • 2May, 2011
  • 1April, 2016
  • 1August, 2016
  • 1December, 2011
  • 1February, 2017
  • 1June, 2017
  • 1May, 2017
  • 1October, 2015
Available data
  • 908fastq
  • 856bam
  • 851bigWig
  • 741bed narrowPeak
  • 739bigBed narrowPeak
  • 407bed broadPeak
  • 329bigBed broadPeak
  • 195tagAlign
  • 14tsv
  • 12sra
  • 12tar
  • 8bigBed bed3+
  • 8gtf
  • 5bed bed9
  • 5bed bedRnaElements
  • 5bigBed bed9
  • 5bigBed bedRnaElements
  • 3bed tss_peak
  • 3bigBed tss_peak
  • 3gff gff3
  • 2bed idr_peak
  • 2bigBed idr_peak
  • 2csfasta
  • 2csqual
  • 1bed bedMethyl
  • 1bigBed bedMethyl
  • 1vcf
Organism
  • 519Homo sapiens
  • 371Mus musculus
  • 48Drosophila melanogaster
  • 7Caenorhabditis elegans
Biosample type
  • 322immortalized cell line
  • 310tissue
  • 138primary cell
  • 73stem cell
  • 72in vitro differentiated cells
  • 22whole organisms
  • 8induced pluripotent stem cell line
Organ
  • 69brain
  • 45embryonic structure
  • 36connective tissue
  • 30heart
  • 29liver
  • 27intestine
  • 24skin of body
  • 21lung
  • 20kidney
  • 17mammary gland
  • 15small intestine
  • 12bone element
  • 11blood vessel
  • 11stomach
  • 9spleen
  • 8gonad
  • 7extraembryonic component
  • 7vein
  • 4ovary
  • 4penis
  • 4testis
  • 3adipose tissue
  • 3large intestine
  • 3muscle organ
  • 2esophagus
  • 1artery
  • 1bronchus
  • 1eye
  • 1mouth
  • 1pancreas
  • 1placenta
  • 1spinal cord
Project
  • 723ENCODE
  • 166Roadmap
  • 47modENCODE
  • 8modERN
  • 1GGR
Genome assembly (visualization)
  • 371hg19
  • 332GRCh38
  • 331mm10
  • 135mm9
  • 5ce10
  • 5ce11
  • 3dm3
  • 3dm6
Audit category:
  • 29control extremely low read depth
  • 17extremely low read depth
  • 6extremely low read length
Audit category:
  • 256insufficient read depth
  • 217control insufficient read depth
  • 128missing controlled_by
  • 44poor library complexity
  • 43control low read depth
  • 43insufficient read length
  • 38severe bottlenecking
  • 14insufficient replicate concordance
  • 4partially characterized antibody
  • 2unreplicated experiment
  • 1antibody not characterized to standard
  • 1insufficient coverage
  • 1missing RNA fragment size
  • 1missing spikeins
  • 1uncharacterized antibody
Audit category:
  • 2781low read length
  • 2377mild to moderate bottlenecking
  • 1798low read depth
  • 1068moderate library complexity
  • 945inconsistent platforms
  • 828inconsistent control read length
  • 730control low read depth
  • 560antibody characterized with exemption
  • 467mixed read lengths
  • 382insufficient read depth
  • 335borderline replicate concordance
  • 306missing external identifiers
  • 241inconsistent target of control experiment
  • 165low spot score
  • 148mixed run types
  • 128inconsistent control run_type
  • 110missing spikeins
  • 89low replicate concordance
  • 89missing genotype
  • 9missing tag construct
  • 1high lambda C methylation ratio
BIOSAMPLE
ASSAY

945 results

search-icontable-tab-icon
Clear Filters
ChIP-seq
polyA mRNA RNA-seq
CAGE
Repli-chip
ATAC-seq
WGBS
genotyping HTS
microRNA-seq
total RNA-seq
immortalized cell line
K5626612
MEL cell line51
CH12.LX31
HepG228
GM128782421
tissue
liver28
heart26
limb20
kidney19
embryonic facial prominence18
primary cell
IMR-90161
mammary epithelial cell16
astrocyte14
fibroblast of dermis14
megakaryocyte91
stem cell
H1-hESC521
H99
ES-Bruce45
ES-E145
hematopoietic stem cell1
in vitro differentiated cells
mesenchymal stem cell241
neuronal stem cell19
mesendoderm8
trophoblast cell5
ectodermal cell11
whole organisms
whole organism1027
carcass3
induced pluripotent stem cell line
iPS-20b6
iPS DF 19.111
iPS DF 6.91
  • Contact
  • Terms of Use
  • Submitter sign-in

©2017 Stanford University.

  • ENCODE
  • UC Santa Cruz
  • Stanford University