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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
563
ChIP-seq
235
total RNA-seq
61
ATAC-seq
11
pCHi-C
7
Hi-C
4
GRO-seq
3
DNase-seq
2
Capture-C
2
single cell RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
Assay category
563
DNA binding
237
Transcription
64
DNA accessibility
7
3D chromatin structure
1
DNA methylation
Target of assay
387
transcription factor
127
histone
127
histone modification
108
control
89
recombinant protein
70
RNA binding protein
broad histone mark
62
narrow histone mark
33
chromatin remodeller
2
other context
2
other post-translational modification
Date released
307
November, 2017
122
February, 2021
106
May, 2021
61
November, 2018
48
August, 2017
41
August, 2021
34
October, 2019
32
December, 2017
31
February, 2018
28
December, 2018
23
January, 2019
19
March, 2020
15
November, 2019
14
February, 2023
5
January, 2018
2
December, 2019
1
August, 2018
1
May, 2020
1
October, 2022
Available data
818
bam
703
bigWig
529
fastq
465
bed narrowPeak
355
bigBed narrowPeak
241
tsv
52
bed broadPeak
52
bigBed broadPeak
40
tagAlign
22
bed bed3+
8
bedpe bed3+
6
bed bed3
5
hic
4
bed bedgraph
3
tar
2
ibed
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
Organism
889
Homo sapiens
Biosample type
2055
tissue
597
cell line
466
primary cell
294
in vitro differentiated cells
7
stem cell
Organ
370
liver
84
epithelium
79
pancreas
73
connective tissue
67
heart
66
artery
66
blood vessel
66
vasculature
61
blood
61
bodily fluid
33
embryo
17
kidney
1
adipose tissue
1
mammary gland
Project
887
AMP
4
T1D
Genome assembly (visualization)
747
hg19
676
GRCh38
4
hg18
Lab
891
AMP-T2D consortium
42
Kyle Gaulton, UCSD
33
Bing Ren, UCSD
7
Struan F.A. Grant, CHOP
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
193
inconsistent ontology term
2
audit script error
1
inconsistent control
1
inconsistent replicate
Audit category:
19
missing controlled_by
Audit category:
32
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_title!
RNA microarray
target.investigated_as!
broad histone mark
BIOSAMPLE
ASSAY
891 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
Hi-C
GRO-seq
DNase-seq
Capture-C
single cell RNA-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
cell line
HepG2
352
5
1
2
1
1
smooth muscle cell of the coronary artery
6
52
8
EndoC_BH1
9
33
19
1
2
1
GM12878
60
1
Panc1
9
1
1
+ See 11 more…
in vitro differentiated cells
cardiomyocytes
3
59
adipocyte
47
5
7
1
neural progenitor cell
14
7
10
cardiac precursors (cardiac muscle cell)
19
1
1
pancreatic endoderm
14
4
1
+ See 28 more…
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