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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
446
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
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
446
DNA binding
82
Transcription
10
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
360
transcription factor
89
recombinant protein
72
control
64
RNA binding protein
30
chromatin remodeller
19
histone
19
histone modification
narrow histone mark
9
broad histone mark
2
other context
2
other post-translational modification
Date released
308
November, 2017
70
February, 2021
61
November, 2018
40
August, 2021
28
December, 2018
22
January, 2019
14
October, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
510
bam
455
bigWig
419
fastq
373
bed narrowPeak
340
bigBed narrowPeak
85
tsv
52
bed broadPeak
52
bigBed broadPeak
15
tagAlign
3
tar
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hic
1
txt
1
vcf
Organism
556
Homo sapiens
Biosample type
1806
tissue
627
primary cell
559
cell line
336
in vitro differentiated cells
9
stem cell
Organ
392
liver
pancreas
72
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
18
kidney
8
embryo
1
mammary gland
Project
552
AMP
5
T1D
2
community
Genome assembly (visualization)
461
hg19
401
GRCh38
Lab
520
AMP-T2D consortium
32
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
16
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
21
inconsistent control read length
8
inconsistent control run_type
assay_title!
DNase-seq
snDrop-seq
organ_slims!
pancreas
target.investigated_as!
narrow histone mark
BIOSAMPLE
ASSAY
559 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
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
369
14
1
2
2
2
1
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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