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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
61
ChIP-seq
9
ATAC-seq
9
total RNA-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Hi-C
2
HiChIP
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
61
DNA binding
11
Transcription
9
DNA accessibility
2
3D chromatin structure
1
DNA sequencing
Target of assay
56
control
5
transcription factor
2
RNA binding protein
1
recombinant protein
Date released
47
November, 2017
20
August, 2021
13
February, 2021
October, 2019
5
February, 2023
4
March, 2020
4
November, 2018
3
January, 2019
2
March, 2023
1
December, 2018
1
May, 2020
1
October, 2022
Available data
504
bam
bigWig
427
fastq
375
bed narrowPeak
347
bigBed narrowPeak
81
tsv
58
bed broadPeak
58
bigBed broadPeak
20
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
98
Homo sapiens
Biosample type
908
tissue
299
primary cell
127
in vitro differentiated cells
101
cell line
7
stem cell
Organ
69
liver
epithelium
29
pancreas
10
artery
10
blood vessel
10
heart
10
vasculature
6
blood
6
bodily fluid
4
kidney
1
mammary gland
Project
94
AMP
5
T1D
2
community
Genome assembly (visualization)
11
hg19
9
GRCh38
Lab
74
AMP-T2D consortium
20
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
3
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
files.file_type!
bigWig
organ_slims!
epithelium
month_released!
October, 2019
BIOSAMPLE
ASSAY
101 results
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ChIP-seq
ATAC-seq
total RNA-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
52
1
9
2
2
2
1
smooth muscle cell of the coronary artery
2
8
GM12878
6
EndoC_BH1
3
2
EndoC-BH1
1
1
HEK293T
2
MCF-7
1
MIN6
1
RCC 7860 VHL
1
RCC 7860 vector
1
Synthesized DNA
1
fibroblast cell line
1
iPSC derived cell line
1
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