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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
365
ChIP-seq
113
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
HiChIP
1
DNase-seq
1
WGBS
1
whole genome sequencing assay
Assay category
365
DNA binding
113
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
317
transcription factor
89
recombinant protein
83
control
RNA binding protein
26
chromatin remodeller
24
histone
24
histone modification
13
narrow histone mark
11
broad histone mark
3
nucleotide modification
1
other context
1
other post-translational modification
Date released
227
November, 2017
96
February, 2021
43
August, 2021
40
November, 2018
29
October, 2019
26
December, 2018
21
May, 2021
17
January, 2019
15
November, 2019
11
March, 2020
6
November, 2020
5
February, 2023
1
January, 2018
1
May, 2020
Available data
518
bam
459
bigWig
364
fastq
341
bed narrowPeak
294
bigBed narrowPeak
119
tsv
bed broadPeak
55
bigBed broadPeak
20
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
2
tar
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
vcf
Organism
538
Homo sapiens
Biosample type
2533
tissue
1034
primary cell
538
cell line
382
in vitro differentiated cells
8
stem cell
Organ
293
liver
89
pancreas
77
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
51
blood
51
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
529
AMP
9
T1D
Genome assembly (visualization)
413
hg19
364
GRCh38
Lab
494
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Audit category:
91
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
11
missing controlled_by
Audit category:
9
inconsistent control read length
5
inconsistent control run_type
1
inconsistent assembly
files.file_type!
bed broadPeak
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
538 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
DNase-seq
WGBS
whole genome sequencing assay
cell line
HepG2
270
14
1
2
2
2
1
1
EndoC_BH1
14
33
19
6
1
3
2
2
smooth muscle cell of the coronary artery
6
52
8
GM12878
50
1
Panc1
13
1
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