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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
459
ChIP-seq
10
ATAC-seq
4
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
DNase-seq
2
Hi-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
pCHi-C
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
459
DNA binding
12
DNA accessibility
2
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
353
transcription factor
82
recombinant protein
75
control
64
RNA binding protein
30
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
28
December, 2018
24
August, 2021
18
February, 2021
18
January, 2019
15
October, 2019
6
February, 2023
2
March, 2023
1
January, 2018
1
October, 2022
Available data
520
bam
464
bigWig
427
fastq
383
bed narrowPeak
355
bigBed narrowPeak
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
hdf5
1
hic
1
txt
1
vcf
Organism
485
Homo sapiens
Biosample type
1613
tissue
624
primary cell
489
cell line
238
in vitro differentiated cells
6
stem cell
Organ
386
liver
61
blood
61
bodily fluid
15
pancreas
14
artery
14
blood vessel
14
heart
14
vasculature
3
kidney
2
epithelium
Project
482
AMP
5
T1D
2
community
Genome assembly (visualization)
401
hg19
338
GRCh38
Lab
458
AMP-T2D consortium
24
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
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 ontology term
files.file_type!
hdf5
tsv
zippedFastqFolder
BIOSAMPLE
ASSAY
489 results
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ChIP-seq
ATAC-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
DNase-seq
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
pCHi-C
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
1
2
2
1
1
1
GM12878
60
1
Panc1
13
1
smooth muscle cell of the coronary artery
6
8
EndoC_BH1
3
2
1
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