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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
453
ChIP-seq
104
total RNA-seq
29
ATAC-seq
6
pCHi-C
3
Hi-C
2
Capture-C
2
DNase-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
Assay category
453
DNA binding
104
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
338
transcription factor
88
recombinant protein
76
control
62
RNA binding protein
34
histone
34
histone modification
24
chromatin remodeller
18
broad histone mark
16
narrow histone mark
2
other context
2
other post-translational modification
Date released
305
November, 2017
96
February, 2021
58
November, 2018
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
10
August, 2021
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
569
bam
496
bigWig
414
fastq
378
bed narrowPeak
343
bigBed narrowPeak
110
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
600
Homo sapiens
Biosample type
2400
tissue
602
cell line
480
primary cell
334
in vitro differentiated cells
8
stem cell
Organ
357
liver
86
pancreas
73
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
598
AMP
4
T1D
Genome assembly (visualization)
503
hg19
459
GRCh38
Lab
602
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
0
Stephen Parker, UMich
Audit category:
85
inconsistent ontology term
1
inconsistent control
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
BIOSAMPLE
ASSAY
602 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
cell line
HepG2
347
5
1
2
1
1
EndoC_BH1
15
33
19
1
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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