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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
438
ChIP-seq
102
total RNA-seq
29
ATAC-seq
6
MeRIP-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
438
DNA binding
102
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
335
transcription factor
88
recombinant protein
79
control
58
RNA binding protein
22
histone
22
histone modification
19
chromatin remodeller
12
broad histone mark
10
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
294
November, 2017
96
February, 2021
56
November, 2018
30
October, 2019
28
December, 2018
23
January, 2019
20
May, 2021
16
November, 2019
10
August, 2021
8
March, 2020
6
November, 2020
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
552
bam
478
bigWig
401
fastq
364
bed narrowPeak
331
bigBed narrowPeak
108
tsv
46
bed broadPeak
46
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
589
Homo sapiens
Biosample type
2670
tissue
591
cell line
554
primary cell
377
in vitro differentiated cells
6
stem cell
Organ
344
liver
88
pancreas
75
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
591
AMP
9
T1D
2
community
Genome assembly (visualization)
485
hg19
438
GRCh38
Lab
585
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
87
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
8
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
lab.title!
Bing Ren, UCSD
BIOSAMPLE
ASSAY
591 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
cell line
HepG2
334
5
1
2
1
1
EndoC_BH1
13
31
19
6
1
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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