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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
169
ChIP-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
whole genome sequencing assay
Assay category
169
DNA binding
Transcription
31
DNA accessibility
3
3D chromatin structure
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
25
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
7
March, 2020
6
February, 2023
6
November, 2020
1
January, 2018
1
May, 2020
1
October, 2022
Available data
164
bam
155
bed narrowPeak
150
bigWig
107
fastq
106
bigBed narrowPeak
8
tagAlign
6
tsv
3
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bed broadPeak
1
bigBed bedMethyl
1
bigBed broadPeak
hdf5
1
txt
1
vcf
Organism
229
Homo sapiens
Biosample type
1468
tissue
639
primary cell
256
in vitro differentiated cells
231
cell line
8
stem cell
Organ
72
liver
61
blood
61
bodily fluid
58
pancreas
45
epithelium
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
mammary gland
Project
224
AMP
7
T1D
Genome assembly (visualization)
159
hg19
142
GRCh38
Lab
195
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Audit category:
56
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
assay_slims!
Transcription
files.file_type!
hdf5
month_released!
November, 2017
BIOSAMPLE
ASSAY
231 results
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ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
whole genome sequencing assay
cell line
HepG2
63
1
2
2
2
1
1
GM12878
60
1
EndoC_BH1
15
19
6
3
1
2
2
1
Panc1
13
1
smooth muscle cell of the coronary artery
6
8
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