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Experiment Matrix

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

Assay
  • 881ChIP-seq
  • 30polyA mRNA RNA-seq
  • 28CAGE
  • 9Repli-chip
  • 8ATAC-seq
  • 8WGBS
  • 1genotyping HTS
  • 1microRNA-seq
  • 1total RNA-seq
Assay category
  • 881DNA binding
  • 60Transcription
  • 9Replication timing
  • 8DNA accessibility
  • 8DNA methylation
  • 8DNA sequencing
  • 1Genotyping
Target of assay
  • 529histone
  • 529histone modification
  • 314transcription factor
  • 252broad histone mark
  • 217narrow histone mark
  • 78RNA binding protein
  • 58chromatin remodeller
  • 36control
  • 13recombinant protein
  • 5other context
  • 5other post-translational modification
Date released
  • 175July, 2013
  • 96November, 2015
  • 82March, 2012
  • 77August, 2012
  • 66February, 2011
  • 56June, 2015
  • 47February, 2012
  • 47March, 2014
  • 37April, 2012
  • 37March, 2011
  • 34October, 2011
  • 28September, 2012
  • 21July, 2014
  • 20March, 2016
  • 19September, 2011
  • 17July, 2011
  • 15June, 2012
  • 14December, 2014
  • 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
  • 921fastq
  • 859bam
  • 854bigWig
  • 742bed narrowPeak
  • 740bigBed narrowPeak
  • 410bed broadPeak
  • 332bigBed broadPeak
  • 202tagAlign
  • 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
  • 537Homo sapiens
  • 375Mus musculus
  • 48Drosophila melanogaster
  • 7Caenorhabditis elegans
Biosample type
  • 329immortalized cell line
  • 312tissue
  • 139primary cell
  • 81in vitro differentiated cells
  • 76stem cell
  • 22whole organisms
  • 8induced pluripotent stem cell line
Organ
  • 69brain
  • 49embryonic structure
  • 37connective tissue
  • 30heart
  • 29liver
  • 27intestine
  • 24skin of body
  • 21lung
  • 20kidney
  • 17mammary gland
  • 15small intestine
  • 12bone element
  • 11blood vessel
  • 11extraembryonic component
  • 11stomach
  • 9spleen
  • 8gonad
  • 7vein
  • 4ovary
  • 4penis
  • 4testis
  • 3adipose tissue
  • 3large intestine
  • 3muscle organ
  • 2esophagus
  • 1artery
  • 1bronchus
  • 1eye
  • 1mouth
  • 1pancreas
  • 1placenta
  • 1spinal cord
Project
  • 735ENCODE
  • 176Roadmap
  • 47modENCODE
  • 8modERN
  • 1GGR
Genome assembly (visualization)
  • 371hg19
  • 332GRCh38
  • 332mm10
  • 137mm9
  • 5ce10
  • 5ce11
  • 3dm3
  • 3dm6
Audit category:
  • 31control extremely low read depth
  • 18extremely low read depth
  • 6extremely low read length
Audit category:
  • 263insufficient read depth
  • 219control insufficient read depth
  • 142missing controlled_by
  • 45insufficient read length
  • 45poor library complexity
  • 43control low read depth
  • 39severe 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:
  • 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

967 results

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Clear Filters
ChIP-seq
polyA mRNA RNA-seq
CAGE
Repli-chip
ATAC-seq
WGBS
genotyping HTS
microRNA-seq
total RNA-seq
immortalized cell line
K5626912
MEL cell line52
CH12.LX31
HeLa-S329
HepG229
tissue
liver28
heart26
limb22
kidney19
embryonic facial prominence18
primary cell
IMR-90161
mammary epithelial cell16
astrocyte14
fibroblast of dermis14
megakaryocyte91
in vitro differentiated cells
mesenchymal stem cell241
neuronal stem cell22
mesendoderm10
trophoblast cell9
ectodermal cell11
stem cell
H1-hESC531
H910
ES-E146
ES-Bruce45
hematopoietic stem cell1
whole organisms
whole organism1027
carcass3
induced pluripotent stem cell line
iPS-20b6
iPS DF 19.111
iPS DF 6.91
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