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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
113
total RNA-seq
19
ATAC-seq
10
ChIP-seq
6
pCHi-C
5
STARR-seq
Hi-C
3
CRISPR genome editing followed by DNA sequencing
3
MeRIP-seq
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
115
Transcription
19
DNA accessibility
10
DNA binding
1
DNA methylation
1
DNA sequencing
Target of assay
control
9
transcription factor
3
histone
3
histone modification
3
nucleotide modification
2
RNA binding protein
broad histone mark
1
narrow histone mark
1
recombinant protein
Date released
79
February, 2021
25
August, 2021
20
May, 2021
10
March, 2020
9
November, 2017
6
February, 2023
5
January, 2019
4
October, 2019
3
November, 2020
2
March, 2023
2
November, 2018
1
January, 2018
1
May, 2020
1
November, 2019
1
October, 2022
Available data
490
bigWig
488
bam
bed narrowPeak
356
fastq
345
bigBed narrowPeak
119
tsv
51
bed broadPeak
51
bigBed broadPeak
10
tagAlign
3
tar
2
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
1
vcf
Organism
165
Homo sapiens
Biosample type
1540
tissue
738
primary cell
202
in vitro differentiated cells
169
cell line
7
stem cell
Organ
58
epithelium
57
pancreas
52
artery
52
blood vessel
52
heart
52
vasculature
30
liver
8
embryo
8
kidney
1
blood
1
bodily fluid
1
mammary gland
Project
160
AMP
7
T1D
2
community
Genome assembly (visualization)
113
hg19
105
GRCh38
Lab
144
AMP-T2D consortium
15
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
3
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
62
inconsistent ontology term
Audit category:
1
missing controlled_by
Audit category:
1
inconsistent control read length
assay_title!
Hi-C
files.file_type!
bed narrowPeak
target.investigated_as!
broad histone mark
control
BIOSAMPLE
ASSAY
169 results
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total RNA-seq
ATAC-seq
ChIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
MeRIP-seq
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
EndoC_BH1
33
18
3
3
2
2
1
smooth muscle cell of the coronary artery
52
HepG2
14
10
2
2
1
1
H1-hESC
8
EndoC-BH1
1
1
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