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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
483
ChIP-seq
109
total RNA-seq
13
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
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
483
DNA binding
111
Transcription
13
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
37
histone
37
histone modification
30
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
61
November, 2018
44
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
May, 2021
16
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
575
bam
515
bigWig
427
fastq
401
bed narrowPeak
353
bigBed narrowPeak
115
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
635
Homo sapiens
Biosample type
2519
tissue
851
primary cell
639
cell line
261
in vitro differentiated cells
10
stem cell
Organ
401
liver
70
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
57
epithelium
18
kidney
8
embryo
1
mammary gland
Project
629
AMP
8
T1D
2
community
Genome assembly (visualization)
523
hg19
457
GRCh38
Lab
592
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
71
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
May, 2021
assay_title!
DNase-seq
BIOSAMPLE
ASSAY
639 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
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
EndoC_BH1
14
29
3
6
1
3
2
2
1
GM12878
60
1
Panc1
13
1
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