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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
251
ChIP-seq
124
total RNA-seq
42
ATAC-seq
6
pCHi-C
4
GRO-seq
4
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
DNase-seq
3
Hi-C
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
251
DNA binding
126
Transcription
45
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
136
histone
136
histone modification
110
control
82
recombinant protein
75
RNA binding protein
69
broad histone mark
66
narrow histone mark
33
chromatin remodeller
2
other context
2
other post-translational modification
Date released
74
November, 2017
73
February, 2021
72
August, 2021
51
May, 2021
46
August, 2017
39
February, 2018
28
December, 2017
19
October, 2019
17
February, 2023
9
January, 2019
5
January, 2018
5
March, 2020
4
November, 2018
3
December, 2018
2
March, 2023
1
August, 2018
1
May, 2020
1
October, 2022
Available data
335
bam
248
bigWig
194
fastq
129
bed narrowPeak
121
tsv
51
tagAlign
42
bigBed narrowPeak
20
bed bed3+
16
bed broadPeak
16
bigBed broadPeak
6
bed bed3
6
bed bedgraph
3
txt
2
bedpe bed3+
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
hic
1
vcf
Organism
446
Homo sapiens
Biosample type
2592
tissue
1027
primary cell
233
in vitro differentiated cells
217
cell line
9
stem cell
Organ
117
liver
71
connective tissue
63
heart
62
artery
62
blood vessel
62
vasculature
28
embryo
19
epithelium
18
pancreas
10
blood
10
bodily fluid
4
kidney
1
adipose tissue
1
mammary gland
Project
443
AMP
5
T1D
2
community
Genome assembly (visualization)
281
hg19
238
GRCh38
4
hg18
Lab
380
AMP-T2D consortium
40
Kyle Gaulton, UCSD
22
Bing Ren, UCSD
6
Struan F.A. Grant, CHOP
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
2
audit script error
1
inconsistent replicate
Audit category:
2
missing controlled_by
Audit category:
17
inconsistent control read length
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
target.investigated_as!
transcription factor
BIOSAMPLE
ASSAY
450 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
GRO-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
DNase-seq
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
in vitro differentiated cells
adipocyte
45
5
8
1
1
embryonic stem cell
28
7
6
1
neural progenitor cell
21
7
10
pancreatic endoderm
15
4
1
hepatocyte
13
+ See 18 more…
cell line
HepG2
81
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
2
52
8
Panc1
13
1
1
GM12878
9
1
H1-hESC
8
+ See 9 more…
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