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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
455
ChIP-seq
111
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
2
Capture-C
2
Hi-C
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
whole genome sequencing assay
Assay category
455
DNA binding
111
Transcription
30
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
336
transcription factor
89
recombinant protein
83
control
63
RNA binding protein
36
histone
36
histone modification
28
chromatin remodeller
19
broad histone mark
17
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
95
February, 2021
61
November, 2018
44
August, 2021
December, 2018
28
October, 2019
23
January, 2019
20
May, 2021
16
November, 2019
8
March, 2020
6
November, 2020
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
551
bam
491
bigWig
399
fastq
375
bed narrowPeak
328
bigBed narrowPeak
117
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
618
Homo sapiens
Biosample type
2468
tissue
620
cell line
522
primary cell
369
in vitro differentiated cells
5
stem cell
Organ
399
liver
86
pancreas
75
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
34
blood
34
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
620
AMP
9
T1D
2
community
Genome assembly (visualization)
496
hg19
431
GRCh38
Lab
580
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
88
inconsistent ontology term
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
files.file_type!
bed bed3+
month_released!
December, 2018
BIOSAMPLE
ASSAY
620 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
STARR-seq
pCHi-C
Capture-C
Hi-C
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
whole genome sequencing assay
cell line
HepG2
378
14
1
2
1
1
1
1
EndoC_BH1
13
31
19
6
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
33
1
Panc1
13
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