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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
123
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
pCHi-C
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
123
DNA binding
30
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
74
November, 2017
19
October, 2019
17
May, 2021
16
August, 2021
14
November, 2019
13
February, 2021
6
February, 2023
6
November, 2020
4
January, 2019
4
November, 2018
3
December, 2018
2
March, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
233
bam
166
bigWig
tsv
90
fastq
52
bed narrowPeak
27
bigBed narrowPeak
15
bed broadPeak
15
bigBed broadPeak
15
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
178
Homo sapiens
Biosample type
1572
tissue
808
primary cell
214
in vitro differentiated cells
182
cell line
6
stem cell
Organ
89
liver
57
pancreas
43
epithelium
10
artery
10
blood
10
blood vessel
10
bodily fluid
10
heart
10
vasculature
6
kidney
Project
173
AMP
7
T1D
2
community
Genome assembly (visualization)
73
hg19
51
GRCh38
Lab
155
AMP-T2D consortium
14
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
45
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
11
inconsistent control read length
1
inconsistent assembly
files.file_type!
tsv
target.investigated_as!
transcription factor
BIOSAMPLE
ASSAY
182 results
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ChIP-seq
ATAC-seq
MeRIP-seq
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
pCHi-C
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
81
1
2
2
1
1
1
EndoC_BH1
14
18
6
1
3
2
2
1
Panc1
13
1
1
GM12878
9
1
smooth muscle cell of the coronary artery
2
8
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