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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
399
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
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
399
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
346
transcription factor
88
recombinant protein
83
control
RNA binding protein
27
histone
27
histone modification
19
chromatin remodeller
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
265
November, 2017
96
February, 2021
43
August, 2021
36
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
498
bam
439
bigWig
344
fastq
323
bed narrowPeak
276
bigBed narrowPeak
119
tsv
44
bed broadPeak
44
bigBed broadPeak
9
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
2
tar
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
573
Homo sapiens
Biosample type
2708
tissue
1073
primary cell
577
cell line
366
in vitro differentiated cells
8
stem cell
Organ
327
liver
91
pancreas
78
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
51
blood
51
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
566
AMP
9
T1D
2
community
Genome assembly (visualization)
448
hg19
389
GRCh38
Lab
531
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:
inconsistent control read length
5
inconsistent control run_type
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
577 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
304
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
6
52
8
GM12878
50
1
Panc1
13
1
1
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