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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
419
ChIP-seq
113
total RNA-seq
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
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
419
DNA binding
115
Transcription
4
3D chromatin structure
2
DNA accessibility
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
87
February, 2021
43
August, 2021
40
November, 2018
30
October, 2019
26
December, 2018
17
January, 2019
14
November, 2019
9
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
508
bam
456
bigWig
364
fastq
331
bed narrowPeak
294
bigBed narrowPeak
118
tsv
55
bed broadPeak
55
bigBed broadPeak
20
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
2
tar
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
564
Homo sapiens
Biosample type
2488
tissue
763
primary cell
568
cell line
341
in vitro differentiated cells
10
stem cell
Organ
346
liver
72
pancreas
59
epithelium
58
artery
58
blood vessel
58
heart
58
vasculature
50
blood
50
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
557
AMP
9
T1D
2
community
Genome assembly (visualization)
455
hg19
396
GRCh38
Lab
522
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:
72
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!
ATAC-seq
files.file_type!
zippedFastqFolder
organ_slims!
pericardium
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
568 results
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ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
324
14
2
2
2
1
1
EndoC_BH1
14
33
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
GM12878
50
Panc1
13
1
1
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