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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
123
ChIP-seq
113
total RNA-seq
28
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
123
DNA binding
115
Transcription
30
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
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
91
February, 2021
74
November, 2017
33
August, 2021
23
October, 2019
21
May, 2021
15
November, 2019
11
March, 2020
9
January, 2019
6
February, 2023
6
November, 2020
4
November, 2018
3
December, 2018
2
March, 2023
January, 2018
1
May, 2020
1
October, 2022
Available data
233
bam
165
bigWig
119
tsv
90
fastq
52
bed narrowPeak
27
bigBed narrowPeak
15
bed broadPeak
15
bigBed broadPeak
15
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
296
Homo sapiens
Biosample type
2681
tissue
1078
primary cell
341
in vitro differentiated cells
300
cell line
9
stem cell
Organ
104
liver
91
pancreas
78
epithelium
62
artery
62
blood vessel
62
heart
62
vasculature
12
kidney
9
blood
9
bodily fluid
8
embryo
1
mammary gland
Project
289
AMP
9
T1D
2
community
Genome assembly (visualization)
177
hg19
155
GRCh38
Lab
264
AMP-T2D consortium
23
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
84
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
11
inconsistent control read length
1
inconsistent assembly
month_released!
January, 2018
target.investigated_as!
transcription factor
BIOSAMPLE
ASSAY
300 results
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ChIP-seq
total RNA-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
81
14
1
2
2
2
1
1
EndoC_BH1
14
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
2
52
8
Panc1
13
1
1
GM12878
9
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