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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
419
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
419
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
chromatin remodeller
12
broad histone mark
10
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
285
November, 2017
96
February, 2021
54
November, 2018
30
October, 2019
26
December, 2018
20
May, 2021
17
January, 2019
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
533
bam
459
bigWig
382
fastq
345
bed narrowPeak
312
bigBed narrowPeak
108
tsv
43
bed broadPeak
43
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
570
Homo sapiens
Biosample type
2668
tissue
572
cell line
553
primary cell
376
in vitro differentiated cells
6
stem cell
Organ
335
liver
88
pancreas
75
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
51
blood
51
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
572
AMP
9
T1D
2
community
Genome assembly (visualization)
466
hg19
420
GRCh38
Lab
566
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
87
inconsistent ontology term
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
inconsistent control read length
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
lab.title!
Bing Ren, UCSD
target.investigated_as!
chromatin remodeller
BIOSAMPLE
ASSAY
572 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
325
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
50
1
Panc1
13
1
1
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