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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
112
ChIP-seq
29
ATAC-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
3
MeRIP-seq
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
112
DNA binding
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
88
recombinant protein
83
control
59
RNA binding protein
27
histone
27
histone modification
19
chromatin remodeller
14
narrow histone mark
13
broad histone mark
nucleotide modification
2
other context
2
other post-translational modification
Date released
91
February, 2021
63
November, 2017
33
August, 2021
23
October, 2019
21
May, 2021
15
November, 2019
11
March, 2020
9
January, 2019
6
February, 2023
4
November, 2018
3
December, 2018
3
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
222
bam
155
bigWig
119
tsv
79
fastq
43
bed narrowPeak
18
bigBed narrowPeak
4
bed broadPeak
4
bigBed broadPeak
4
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
283
Homo sapiens
Biosample type
2512
tissue
1022
primary cell
338
in vitro differentiated cells
287
cell line
8
stem cell
Organ
93
liver
88
pancreas
75
epithelium
62
artery
62
blood vessel
62
heart
62
vasculature
12
kidney
10
blood
10
bodily fluid
8
embryo
1
mammary gland
Project
276
AMP
9
T1D
2
community
Genome assembly (visualization)
167
hg19
146
GRCh38
Lab
254
AMP-T2D consortium
23
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
3
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
81
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
inconsistent control read length
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
month_released!
June, 2019
target.investigated_as!
nucleotide modification
transcription factor
BIOSAMPLE
ASSAY
287 results
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total RNA-seq
ChIP-seq
ATAC-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
MeRIP-seq
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
70
1
2
2
2
1
1
EndoC_BH1
33
14
19
1
3
3
2
2
1
smooth muscle cell of the coronary artery
52
2
8
Panc1
13
1
1
GM12878
9
1
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