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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
80
total RNA-seq
10
ATAC-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Hi-C
2
HiChIP
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
455
DNA binding
82
Transcription
11
DNA accessibility
2
3D chromatin structure
1
DNA methylation
Target of assay
359
transcription factor
89
recombinant protein
72
control
64
RNA binding protein
29
chromatin remodeller
19
histone
19
histone modification
10
narrow histone mark
9
broad histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
61
November, 2018
41
August, 2021
27
December, 2018
23
January, 2019
15
October, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
518
bam
465
bigWig
426
fastq
382
bed narrowPeak
347
bigBed narrowPeak
85
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
vcf
Organism
565
Homo sapiens
Biosample type
2245
tissue
742
primary cell
568
cell line
391
in vitro differentiated cells
10
stem cell
Organ
400
liver
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
561
AMP
5
T1D
2
community
Genome assembly (visualization)
471
hg19
408
GRCh38
Lab
528
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
16
inconsistent ontology term
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
audit.ERROR.category!
inconsistent control
files.file_type!
vcf
organ_slims!
pancreas
BIOSAMPLE
ASSAY
568 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
378
14
1
2
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
H1-hESC
8
EndoC_BH1
3
2
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