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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
447
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
1
whole genome sequencing assay
Assay category
447
DNA binding
82
Transcription
11
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
10
narrow histone mark
broad histone mark
2
other context
2
other post-translational modification
Date released
307
November, 2017
70
February, 2021
61
November, 2018
41
August, 2021
28
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
511
bam
457
bigWig
419
fastq
375
bed narrowPeak
341
bigBed narrowPeak
85
tsv
50
bed broadPeak
50
bigBed broadPeak
14
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
558
Homo sapiens
Biosample type
2010
tissue
647
primary cell
561
cell line
335
in vitro differentiated cells
9
stem cell
Organ
392
liver
pancreas
72
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
554
AMP
5
T1D
2
community
Genome assembly (visualization)
463
hg19
402
GRCh38
Lab
521
AMP-T2D consortium
33
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:
13
missing controlled_by
Audit category:
20
inconsistent control read length
8
inconsistent control run_type
assay_title!
CRISPR genome editing followed by sgRNA sequencing
organ_slims!
pancreas
target.investigated_as!
broad histone mark
BIOSAMPLE
ASSAY
561 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
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
60
1
H1-hESC
8
EndoC_BH1
3
2
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