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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
366
ChIP-seq
113
total RNA-seq
28
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
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
366
DNA binding
115
Transcription
28
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
266
transcription factor
89
recombinant protein
77
control
51
RNA binding protein
23
histone
23
histone modification
16
chromatin remodeller
12
narrow histone mark
11
broad histone mark
3
nucleotide modification
1
other context
1
other post-translational modification
Date released
257
November, 2017
96
February, 2021
46
November, 2018
44
August, 2021
28
October, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
5
January, 2019
2
March, 2023
1
December, 2018
1
May, 2020
1
October, 2022
Available data
520
bam
465
bigWig
367
fastq
348
bed narrowPeak
299
bigBed narrowPeak
119
tsv
58
bed broadPeak
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
537
Homo sapiens
Biosample type
2599
tissue
1028
primary cell
541
cell line
393
in vitro differentiated cells
10
stem cell
Organ
343
liver
91
pancreas
78
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
blood
61
bodily fluid
18
kidney
8
embryo
1
mammary gland
Project
530
AMP
9
T1D
2
community
Genome assembly (visualization)
415
hg19
364
GRCh38
Lab
494
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
92
inconsistent ontology term
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
13
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_title!
DNase-seq
organ_slims!
blood
files.file_type!
bigBed broadPeak
BIOSAMPLE
ASSAY
541 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
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
320
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
Panc1
13
1
H1-hESC
8
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