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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
464
ChIP-seq
113
total RNA-seq
29
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
whole genome sequencing assay
Assay category
464
DNA binding
113
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
89
recombinant protein
79
control
65
RNA binding protein
30
chromatin remodeller
27
histone
27
histone modification
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
303
November, 2017
88
February, 2021
61
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
1
January, 2018
1
May, 2020
1
October, 2022
Available data
582
bam
522
bigWig
427
fastq
404
bed narrowPeak
355
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
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
638
Homo sapiens
Biosample type
2534
tissue
988
primary cell
640
cell line
354
in vitro differentiated cells
8
stem cell
Organ
389
liver
92
pancreas
79
epithelium
61
blood
61
bodily fluid
60
artery
60
blood vessel
60
heart
60
vasculature
19
kidney
8
embryo
1
mammary gland
Project
631
AMP
9
T1D
Genome assembly (visualization)
513
hg19
450
GRCh38
Lab
595
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:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
files.file_type!
tagAlign
lab.title!
Anna Gloyn, Oxford
month_released!
March, 2019
BIOSAMPLE
ASSAY
640 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
whole genome sequencing assay
cell line
HepG2
366
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
GM12878
60
1
smooth muscle cell of the coronary artery
52
8
Panc1
13
1
1
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