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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
357
ChIP-seq
109
total RNA-seq
13
ATAC-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
357
DNA binding
111
Transcription
15
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
recombinant protein
80
control
65
RNA binding protein
37
histone
histone modification
30
chromatin remodeller
19
broad histone mark
18
narrow histone mark
2
other context
2
other post-translational modification
Date released
234
November, 2017
96
February, 2021
45
November, 2018
41
August, 2021
28
December, 2018
22
January, 2019
May, 2021
16
October, 2019
10
March, 2020
6
February, 2023
6
November, 2019
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
454
bam
393
bigWig
329
fastq
281
bed narrowPeak
254
bigBed narrowPeak
115
tsv
45
bed broadPeak
45
bigBed broadPeak
9
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
505
Homo sapiens
Biosample type
2105
tissue
763
primary cell
509
cell line
171
in vitro differentiated cells
8
stem cell
Organ
301
liver
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
47
pancreas
41
epithelium
12
kidney
8
embryo
1
mammary gland
Project
500
AMP
7
T1D
2
community
Genome assembly (visualization)
404
hg19
340
GRCh38
Lab
471
AMP-T2D consortium
31
Bing Ren, UCSD
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
47
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
11
missing controlled_by
Audit category:
14
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
lab.title!
Rohit N. Kulkarni, M.D., Ph.D.
month_released!
May, 2021
target.investigated_as!
histone modification
recombinant protein
BIOSAMPLE
ASSAY
509 results
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ChIP-seq
total RNA-seq
ATAC-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
278
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
EndoC_BH1
3
29
3
1
3
2
2
1
H1-hESC
8
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