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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
446
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
1
whole genome sequencing assay
Assay category
446
DNA binding
111
Transcription
29
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
354
transcription factor
82
recombinant protein
74
control
65
RNA binding protein
31
histone
31
histone modification
30
chromatin remodeller
16
narrow histone mark
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
307
November, 2017
96
February, 2021
61
November, 2018
43
August, 2021
28
December, 2018
October, 2019
23
January, 2019
21
May, 2021
11
March, 2020
10
November, 2019
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
539
bam
487
bigWig
419
fastq
375
bed narrowPeak
340
bigBed narrowPeak
115
tsv
50
bed broadPeak
50
bigBed broadPeak
14
tagAlign
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
1
vcf
Organism
613
Homo sapiens
Biosample type
2251
tissue
944
primary cell
617
cell line
330
in vitro differentiated cells
9
stem cell
Organ
392
liver
71
epithelium
71
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
8
embryo
4
kidney
1
mammary gland
Project
606
AMP
9
T1D
2
community
Genome assembly (visualization)
495
hg19
431
GRCh38
Lab
571
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:
73
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
20
inconsistent control read length
8
inconsistent control run_type
target.investigated_as!
broad histone mark
month_released!
October, 2019
BIOSAMPLE
ASSAY
617 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
whole genome sequencing assay
cell line
HepG2
369
14
1
2
2
2
1
1
EndoC_BH1
9
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
H1-hESC
8
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