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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
446
ChIP-seq
113
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
446
DNA binding
115
Transcription
29
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
95
February, 2021
61
November, 2018
41
August, 2021
28
December, 2018
22
January, 2019
20
May, 2021
20
October, 2019
10
March, 2020
6
February, 2023
6
November, 2019
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
545
bam
483
bigWig
411
fastq
367
bed narrowPeak
333
bigBed narrowPeak
119
tsv
44
bed broadPeak
44
bigBed broadPeak
9
tagAlign
3
tar
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
616
Homo sapiens
Biosample type
1928
tissue
757
primary cell
620
cell line
264
in vitro differentiated cells
7
stem cell
Organ
382
liver
71
pancreas
66
artery
66
blood vessel
66
epithelium
66
heart
66
vasculature
60
blood
60
bodily fluid
18
kidney
8
embryo
1
mammary gland
Project
611
AMP
7
T1D
2
community
Genome assembly (visualization)
489
hg19
429
GRCh38
Lab
576
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
80
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
assay_title!
DNase-seq
snATAC-seq
files.file_type!
bed bed3+
target.investigated_as!
histone
BIOSAMPLE
ASSAY
620 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
360
14
1
2
1
2
1
1
EndoC_BH1
3
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
H1-hESC
8
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