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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
380
ChIP-seq
113
total RNA-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
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
380
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA sequencing
Target of assay
304
transcription factor
80
control
73
recombinant protein
RNA binding protein
38
histone
38
histone modification
23
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
281
November, 2017
96
February, 2021
43
August, 2021
November, 2018
30
October, 2019
26
December, 2018
21
May, 2021
17
January, 2019
15
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
478
bam
423
bigWig
324
fastq
306
bed narrowPeak
259
bigBed narrowPeak
119
tsv
55
bed broadPeak
55
bigBed broadPeak
20
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
2
tar
1
bed bed3
1
hdf5
1
txt
1
vcf
Organism
553
Homo sapiens
Biosample type
2688
tissue
1077
primary cell
557
cell line
383
in vitro differentiated cells
10
stem cell
Organ
320
liver
91
pancreas
78
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
38
blood
38
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
546
AMP
9
T1D
2
community
Genome assembly (visualization)
435
hg19
370
GRCh38
Lab
511
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
91
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
8
missing controlled_by
Audit category:
16
inconsistent control read length
2
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
RNA binding protein
month_released!
November, 2018
BIOSAMPLE
ASSAY
557 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
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
298
14
1
2
2
2
1
EndoC_BH1
14
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
37
1
Panc1
13
1
1
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