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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
444
ChIP-seq
113
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
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
444
DNA binding
115
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
324
transcription factor
88
recombinant protein
83
control
61
RNA binding protein
37
histone
37
histone modification
22
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
305
November, 2017
96
February, 2021
58
November, 2018
44
August, 2021
30
October, 2019
December, 2018
23
January, 2019
21
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
542
bam
483
bigWig
386
fastq
365
bed narrowPeak
316
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
20
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
617
Homo sapiens
Biosample type
2744
tissue
1044
primary cell
621
cell line
388
in vitro differentiated cells
10
stem cell
Organ
387
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
34
blood
34
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
610
AMP
9
T1D
2
community
Genome assembly (visualization)
491
hg19
432
GRCh38
Lab
574
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:
92
inconsistent ontology term
1
inconsistent replicate
Audit category:
missing controlled_by
Audit category:
21
inconsistent control read length
2
inconsistent control run_type
1
inconsistent assembly
audit.NOT_COMPLIANT.category!
missing controlled_by
month_released!
December, 2018
BIOSAMPLE
ASSAY
621 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
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
365
14
1
2
2
1
1
1
EndoC_BH1
15
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
33
1
Panc1
13
1
1
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