Toggle navigation
ENCODE
Data
Matrix
Search
Search by region
Reference epigenomes
Publications
Encyclopedia
About
Matrix
Search
Materials & Methods
Antibodies
Biosamples
Genome references
Standards and guidelines
Ontologies
File formats
Software tools
Pipelines
Release policy
Data access
Help
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
57
siRNA RNA-seq
15
ChIP-seq
10
CAGE
1
RIP-seq
Assay category
67
Transcription
15
DNA binding
1
RNA binding
Target of assay
68
RNA binding protein
11
transcription factor
4
histone
4
histone modification
3
narrow histone mark
1
broad histone mark
1
tag
Date released
63
March, 2014
7
March, 2011
6
January, 2012
3
December, 2011
3
July, 2013
1
April, 2012
Available data
79
fastq
57
sam
57
wig
18
bam
17
bigWig
12
bed narrowPeak
12
bigBed narrowPeak
7
bed broadPeak
7
bigBed broadPeak
4
bed bedRnaElements
4
bigBed bedRnaElements
4
gtf
3
sra
1
bed bedGraph
1
csfasta
1
csqual
Organism
59
Drosophila melanogaster
20
Homo sapiens
4
Drosophila pseudoobscura
Biosample type
73
immortalized cell line
4
tissue
3
primary cell
2
whole organisms
1
stem cell
Organ
2
gonad
1
ovary
1
prostate gland
1
testis
Project
63
modENCODE
17
ENCODE
3
Roadmap
Genome assembly (visualization)
1
hg19
Audit category:
1
extremely low read depth
0
missing possible_controls
Audit category:
1472
insufficient read depth
880
control insufficient read depth
624
missing controlled_by
481
insufficient read length
310
unreplicated experiment
224
poor library complexity
213
severe bottlenecking
203
control low read depth
120
insufficient spot score
111
partially characterized antibody
83
missing possible_controls
68
missing RNA fragment size
49
missing documents
47
insufficient replicate concordance
27
antibody not characterized to standard
26
uncharacterized antibody
10
missing spikeins
2
insufficient coverage
2
missing input control
Audit category:
12
low read length
10
mild to moderate bottlenecking
7
moderate library complexity
4
missing external identifiers
4
missing genotype
2
low read depth
BIOSAMPLE
ASSAY
83 results
search-icon
table-tab-icon
Clear Filters
siRNA RNA-seq
ChIP-seq
CAGE
RIP-seq
immortalized cell line
S2-DRSC
57
GM12866
2
GM12867
1
GM12868
1
GM12869
1
+ See 11 more…
tissue
head
1
ovary
1
prostate gland
1
testis
1
primary cell
cortex derived neurospheres
3
whole organisms
carcass
2
stem cell
H1-hESC
1
See all biosamples
Download
Visualize