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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
431
ChIP-seq
109
total RNA-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
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
whole genome sequencing assay
Assay category
431
DNA binding
111
Transcription
29
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
354
transcription factor
82
recombinant protein
74
control
65
RNA binding protein
31
histone
31
histone modification
chromatin remodeller
16
narrow histone mark
15
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
96
February, 2021
54
November, 2018
43
August, 2021
October, 2019
26
December, 2018
21
May, 2021
17
January, 2019
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
523
bam
472
bigWig
397
fastq
359
bed narrowPeak
317
bigBed narrowPeak
115
tsv
54
bed broadPeak
54
bigBed broadPeak
20
tagAlign
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
Organism
597
Homo sapiens
Biosample type
2533
tissue
980
primary cell
601
cell line
383
in vitro differentiated cells
10
stem cell
Organ
380
liver
77
epithelium
77
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
51
blood
51
bodily fluid
8
embryo
4
kidney
1
mammary gland
Project
590
AMP
9
T1D
2
community
Genome assembly (visualization)
480
hg19
416
GRCh38
Lab
555
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
79
inconsistent ontology term
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
15
inconsistent control read length
assay_title!
whole genome sequencing assay
month_released!
October, 2019
September, 2018
target.investigated_as!
chromatin remodeller
BIOSAMPLE
ASSAY
601 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
358
14
1
2
2
2
1
EndoC_BH1
15
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
50
1
H1-hESC
8
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