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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
448
ChIP-seq
108
total RNA-seq
28
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
Hi-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
448
DNA binding
110
Transcription
28
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
353
transcription factor
82
recombinant protein
72
control
64
RNA binding protein
30
chromatin remodeller
21
histone
21
histone modification
12
narrow histone mark
9
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
61
November, 2018
44
August, 2021
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
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
538
bam
490
bigWig
427
fastq
377
bed narrowPeak
347
bigBed narrowPeak
114
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hic
1
txt
1
vcf
Organism
612
Homo sapiens
Biosample type
2494
tissue
1054
primary cell
616
cell line
381
in vitro differentiated cells
10
stem cell
Organ
401
liver
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
61
epithelium
61
pancreas
8
embryo
4
kidney
1
mammary gland
Project
605
AMP
9
T1D
2
community
Genome assembly (visualization)
496
hg19
431
GRCh38
Lab
569
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:
63
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
month_released!
October, 2019
November, 2019
lab.title!
Maike Sander, UCSD
BIOSAMPLE
ASSAY
616 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
Capture-C
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
2
1
1
EndoC_BH1
2
32
18
6
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
H1-hESC
8
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