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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
414
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
414
DNA binding
115
Transcription
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
353
transcription factor
89
recombinant protein
83
control
RNA binding protein
38
histone
38
histone modification
22
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
279
November, 2017
87
February, 2021
43
August, 2021
37
November, 2018
28
October, 2019
26
December, 2018
17
January, 2019
14
November, 2019
9
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
501
bam
449
bigWig
359
fastq
324
bed narrowPeak
287
bigBed narrowPeak
118
tsv
54
bed broadPeak
54
bigBed broadPeak
20
tagAlign
2
bed bed3+
2
bedpe bed3+
2
hic
2
tar
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
557
Homo sapiens
Biosample type
2278
tissue
789
primary cell
561
cell line
340
in vitro differentiated cells
10
stem cell
Organ
341
liver
71
pancreas
58
artery
58
blood vessel
58
epithelium
58
heart
58
vasculature
50
blood
50
bodily fluid
18
kidney
8
embryo
1
mammary gland
Project
550
AMP
9
T1D
2
community
Genome assembly (visualization)
448
hg19
390
GRCh38
Lab
515
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:
72
inconsistent ontology term
1
inconsistent control
Audit category:
7
missing controlled_by
Audit category:
20
inconsistent control read length
inconsistent control run_type
1
inconsistent assembly
assay_slims!
DNA accessibility
audit.WARNING.category!
inconsistent control run_type
organ_slims!
small intestine
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
561 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
319
14
2
2
2
1
1
EndoC_BH1
14
33
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
GM12878
50
Panc1
13
1
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