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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
113
total RNA-seq
104
ChIP-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
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
104
DNA binding
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
91
February, 2021
66
November, 2017
32
August, 2021
21
May, 2021
19
October, 2019
11
March, 2020
9
January, 2019
9
November, 2019
6
February, 2023
6
November, 2020
4
November, 2018
3
December, 2018
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
215
bam
148
bigWig
119
tsv
82
fastq
35
bed narrowPeak
17
bigBed narrowPeak
9
tagAlign
7
bed broadPeak
7
bigBed broadPeak
3
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
278
Homo sapiens
Biosample type
2375
tissue
956
primary cell
289
in vitro differentiated cells
282
cell line
9
stem cell
Organ
95
liver
81
pancreas
72
epithelium
62
artery
62
blood vessel
62
heart
62
vasculature
12
kidney
10
blood
10
bodily fluid
8
embryo
1
mammary gland
Project
271
AMP
9
T1D
2
community
Genome assembly (visualization)
160
hg19
139
GRCh38
Lab
247
AMP-T2D consortium
22
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
78
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
5
inconsistent control read length
1
inconsistent assembly
target.investigated_as!
broad histone mark
transcription factor
organ_slims!
gonad
BIOSAMPLE
ASSAY
282 results
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total RNA-seq
ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
14
72
1
2
2
2
1
1
EndoC_BH1
33
8
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
52
2
8
Panc1
9
1
1
GM12878
9
1
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