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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
408
ChIP-seq
104
total RNA-seq
29
ATAC-seq
6
pCHi-C
3
Hi-C
2
Capture-C
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
408
DNA binding
106
Transcription
30
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
306
transcription factor
89
recombinant protein
76
control
60
RNA binding protein
26
chromatin remodeller
21
histone
21
histone modification
11
narrow histone mark
10
broad histone mark
1
other context
1
other post-translational modification
Date released
257
November, 2017
96
February, 2021
61
November, 2018
29
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
10
August, 2021
2
March, 2023
1
February, 2023
1
January, 2018
1
May, 2020
October, 2022
Available data
582
bam
508
bigWig
427
fastq
390
bed narrowPeak
355
bigBed narrowPeak
110
tsv
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
Organism
554
Homo sapiens
Biosample type
2214
tissue
557
cell line
475
primary cell
339
in vitro differentiated cells
10
stem cell
Organ
312
liver
85
pancreas
73
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
551
AMP
4
T1D
2
community
Genome assembly (visualization)
456
hg19
419
GRCh38
Lab
555
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:
85
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
13
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
files.file_type!
bed broadPeak
month_released!
October, 2022
BIOSAMPLE
ASSAY
557 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
Hi-C
Capture-C
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
302
5
1
2
1
1
EndoC_BH1
15
33
19
1
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
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