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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
169
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
169
DNA binding
30
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
120
transcription factor
31
RNA binding protein
27
control
23
histone
23
histone modification
23
recombinant protein
15
chromatin remodeller
12
narrow histone mark
11
broad histone mark
3
nucleotide modification
Date released
November, 2017
61
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
6
February, 2023
6
November, 2020
2
March, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
268
bam
254
bigWig
155
bed narrowPeak
tsv
112
fastq
106
bigBed narrowPeak
8
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bed broadPeak
1
bigBed bedMethyl
1
bigBed broadPeak
1
hdf5
1
txt
1
vcf
Organism
224
Homo sapiens
Biosample type
1579
tissue
809
primary cell
263
in vitro differentiated cells
228
cell line
6
stem cell
Organ
71
liver
61
blood
61
bodily fluid
58
pancreas
44
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
219
AMP
7
T1D
2
community
Genome assembly (visualization)
159
hg19
143
GRCh38
Lab
190
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
53
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
3
missing controlled_by
Audit category:
5
inconsistent control read length
4
inconsistent control run_type
1
inconsistent assembly
month_released!
November, 2017
files.file_type!
tsv
BIOSAMPLE
ASSAY
228 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
63
1
2
2
1
1
1
GM12878
60
1
EndoC_BH1
15
18
6
1
3
2
2
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
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