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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
465
ChIP-seq
113
total RNA-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
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
465
DNA binding
115
Transcription
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
307
November, 2017
87
February, 2021
61
November, 2018
43
August, 2021
28
December, 2018
24
October, 2019
23
January, 2019
9
March, 2020
9
November, 2019
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
552
bam
499
bigWig
419
fastq
375
bed narrowPeak
343
bigBed narrowPeak
118
tsv
50
bed broadPeak
50
bigBed broadPeak
14
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
608
Homo sapiens
Biosample type
1984
tissue
678
primary cell
612
cell line
295
in vitro differentiated cells
9
stem cell
Organ
391
liver
62
pancreas
60
blood
60
bodily fluid
58
artery
58
blood vessel
58
heart
58
vasculature
53
epithelium
18
kidney
8
embryo
1
mammary gland
Project
601
AMP
9
T1D
2
community
Genome assembly (visualization)
497
hg19
436
GRCh38
Lab
566
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:
67
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
20
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
broad histone mark
assay_slims!
DNA accessibility
BIOSAMPLE
ASSAY
612 results
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ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
369
14
2
2
2
1
1
GM12878
60
smooth muscle cell of the coronary artery
6
52
EndoC_BH1
9
33
6
1
3
2
2
1
Panc1
9
1
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