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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
378
ChIP-seq
113
total RNA-seq
ATAC-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
MeRIP-seq
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
378
DNA binding
115
Transcription
4
3D chromatin structure
2
DNA accessibility
1
DNA methylation
1
DNA sequencing
Target of assay
346
transcription factor
88
recombinant protein
control
59
RNA binding protein
27
histone
27
histone modification
19
chromatin remodeller
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
238
November, 2017
84
February, 2021
53
November, 2018
40
August, 2021
28
December, 2018
21
October, 2019
20
January, 2019
13
November, 2019
9
March, 2020
5
May, 2021
3
November, 2020
2
March, 2023
1
February, 2023
1
May, 2020
1
October, 2022
Available data
480
bigWig
470
bam
370
bed narrowPeak
339
fastq
331
bigBed narrowPeak
118
tsv
46
bed broadPeak
46
bigBed broadPeak
5
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
515
Homo sapiens
Biosample type
2301
tissue
612
primary cell
519
cell line
261
in vitro differentiated cells
7
stem cell
Organ
314
liver
62
pancreas
56
artery
56
blood vessel
56
heart
56
vasculature
55
epithelium
54
blood
54
bodily fluid
16
kidney
8
embryo
1
mammary gland
Project
513
AMP
4
T1D
2
community
Genome assembly (visualization)
478
hg19
432
GRCh38
Lab
484
AMP-T2D consortium
30
Bing Ren, UCSD
Kyle Gaulton, UCSD
3
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
65
inconsistent ontology term
1
inconsistent control
Audit category:
8
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_title!
ATAC-seq
audit.WARNING.category!
inconsistent control read length
lab.title!
Kyle Gaulton, UCSD
target.investigated_as!
control
BIOSAMPLE
ASSAY
519 results
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ChIP-seq
total RNA-seq
pCHi-C
STARR-seq
Hi-C
MeRIP-seq
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
292
14
2
2
2
1
1
smooth muscle cell of the coronary artery
4
52
GM12878
54
EndoC_BH1
13
33
1
3
2
1
Panc1
7
1
1
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