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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
428
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
428
DNA binding
104
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
335
transcription factor
88
recombinant protein
76
control
58
RNA binding protein
24
histone
24
histone modification
19
chromatin remodeller
12
broad histone mark
narrow histone mark
2
other context
2
other post-translational modification
Date released
292
November, 2017
96
February, 2021
56
November, 2018
28
December, 2018
27
October, 2019
22
January, 2019
20
May, 2021
12
November, 2019
10
August, 2021
10
March, 2020
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
544
bam
470
bigWig
398
fastq
354
bed narrowPeak
325
bigBed narrowPeak
110
tsv
45
bed broadPeak
45
bigBed broadPeak
9
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
575
Homo sapiens
Biosample type
2113
tissue
577
cell line
459
primary cell
280
in vitro differentiated cells
6
stem cell
Organ
342
liver
77
pancreas
67
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
575
AMP
2
T1D
Genome assembly (visualization)
477
hg19
430
GRCh38
Lab
577
AMP-T2D consortium
32
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
79
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
narrow histone mark
audit.WARNING.category!
inconsistent control read length
BIOSAMPLE
ASSAY
577 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
332
5
1
2
1
1
smooth muscle cell of the coronary artery
6
52
8
EndoC_BH1
9
33
19
1
2
1
GM12878
59
1
Panc1
10
1
1
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