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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
478
ChIP-seq
61
total RNA-seq
21
ATAC-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
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
whole genome sequencing assay
Assay category
478
DNA binding
61
Transcription
21
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
357
transcription factor
89
recombinant protein
81
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
44
August, 2021
30
February, 2021
28
December, 2018
28
October, 2019
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
1
January, 2018
May, 2020
1
October, 2022
Available data
514
bam
464
bigWig
427
fastq
390
bed narrowPeak
353
bigBed narrowPeak
66
tsv
58
bed broadPeak
58
bigBed broadPeak
14
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
589
Homo sapiens
Biosample type
2337
tissue
908
primary cell
591
cell line
393
in vitro differentiated cells
8
stem cell
Organ
400
liver
91
pancreas
78
epithelium
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
18
kidney
8
embryo
1
mammary gland
Project
582
AMP
9
T1D
Genome assembly (visualization)
464
hg19
398
GRCh38
Lab
546
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Anna Gloyn, Oxford
Audit category:
92
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
assay_title!
DNase-seq
lab.title!
Anna Gloyn, Oxford
month_released!
May, 2020
organ_slims!
artery
BIOSAMPLE
ASSAY
591 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
STARR-seq
pCHi-C
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
whole genome sequencing assay
cell line
HepG2
378
14
1
2
1
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
GM12878
60
1
Panc1
13
1
H1-hESC
8
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