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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
419
ChIP-seq
total RNA-seq
28
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
2
Capture-C
2
DNase-seq
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
419
DNA binding
30
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
281
November, 2017
40
November, 2018
26
August, 2021
26
December, 2018
26
October, 2019
17
February, 2021
17
May, 2021
14
November, 2019
12
January, 2019
7
March, 2020
6
November, 2020
2
March, 2023
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
414
bam
359
fastq
355
bigWig
341
bed narrowPeak
294
bigBed narrowPeak
55
bed broadPeak
55
bigBed broadPeak
20
tagAlign
6
tsv
3
bed bed3+
2
bedpe bed3+
2
hic
2
tar
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
474
Homo sapiens
Biosample type
1673
tissue
689
primary cell
478
cell line
205
in vitro differentiated cells
10
stem cell
Organ
332
liver
58
pancreas
51
blood
51
bodily fluid
44
epithelium
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
mammary gland
Project
474
AMP
2
T1D
2
community
Genome assembly (visualization)
363
hg19
301
GRCh38
Lab
446
AMP-T2D consortium
24
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
55
inconsistent ontology term
1
inconsistent control
Audit category:
11
missing controlled_by
Audit category:
20
inconsistent control read length
5
inconsistent control run_type
1
inconsistent assembly
assay_title!
total RNA-seq
files.file_type!
bed bed3
lab.title!
Kyle Gaulton, UCSD
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
478 results
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ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
324
2
2
2
1
1
GM12878
50
1
EndoC_BH1
14
19
6
1
2
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
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