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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
451
ChIP-seq
77
total RNA-seq
10
ATAC-seq
4
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
pCHi-C
2
Hi-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
451
DNA binding
79
Transcription
11
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
345
transcription factor
82
recombinant protein
75
control
61
RNA binding protein
26
histone
26
histone modification
22
chromatin remodeller
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
311
November, 2017
69
February, 2021
57
November, 2018
41
August, 2021
28
December, 2018
23
January, 2019
15
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
512
bam
456
bigWig
419
fastq
375
bed narrowPeak
347
bigBed narrowPeak
80
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
555
Homo sapiens
Biosample type
2481
tissue
999
primary cell
559
cell line
256
in vitro differentiated cells
6
stem cell
Organ
392
liver
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
14
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
552
AMP
5
T1D
2
community
Genome assembly (visualization)
459
hg19
399
GRCh38
Lab
519
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
26
inconsistent control read length
inconsistent control run_type
audit.ERROR.category!
inconsistent ontology term
audit.WARNING.category!
inconsistent control run_type
files.file_type!
bed bed3+
organ_slims!
large intestine
BIOSAMPLE
ASSAY
559 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
pCHi-C
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
370
14
1
2
1
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
H1-hESC
8
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