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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
405
ChIP-seq
113
total RNA-seq
28
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
405
DNA binding
115
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
310
transcription factor
89
recombinant protein
77
control
55
RNA binding protein
37
histone
37
histone modification
20
chromatin remodeller
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
307
November, 2017
96
February, 2021
46
November, 2018
43
August, 2021
26
October, 2019
21
May, 2021
11
March, 2020
10
November, 2019
6
February, 2023
6
November, 2020
5
January, 2019
2
March, 2023
1
December, 2018
1
May, 2020
1
October, 2022
Available data
504
bam
449
bigWig
359
fastq
333
bed narrowPeak
291
bigBed narrowPeak
119
tsv
51
bed broadPeak
51
bigBed broadPeak
14
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
578
Homo sapiens
Biosample type
2472
tissue
958
primary cell
582
cell line
334
in vitro differentiated cells
8
stem cell
Organ
392
liver
82
pancreas
73
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
571
AMP
9
T1D
2
community
Genome assembly (visualization)
457
hg19
394
GRCh38
Lab
536
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:
86
inconsistent ontology term
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
20
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
January, 2018
organ_slims!
bodily fluid
target.investigated_as!
broad histone mark
BIOSAMPLE
ASSAY
582 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
369
14
1
2
2
2
1
1
EndoC_BH1
9
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
Panc1
9
1
1
H1-hESC
8
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