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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
151
ChIP-seq
104
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
151
DNA binding
106
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
109
transcription factor
30
RNA binding protein
23
control
23
recombinant protein
20
histone
20
histone modification
15
chromatin remodeller
10
broad histone mark
10
narrow histone mark
3
nucleotide modification
Date released
November, 2017
96
February, 2021
61
November, 2018
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
10
August, 2021
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
268
bam
240
bigWig
141
bed narrowPeak
112
fastq
110
tsv
106
bigBed narrowPeak
8
tagAlign
3
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bed broadPeak
1
bedpe bed3+
1
bigBed bedMethyl
1
bigBed broadPeak
1
hdf5
1
hic
1
txt
Organism
309
Homo sapiens
Biosample type
2651
tissue
1079
primary cell
394
in vitro differentiated cells
313
cell line
10
stem cell
Organ
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
55
liver
17
kidney
8
embryo
1
mammary gland
Project
302
AMP
9
T1D
2
community
Genome assembly (visualization)
249
hg19
247
GRCh38
Lab
300
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
91
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
3
missing controlled_by
Audit category:
5
inconsistent control read length
4
inconsistent control run_type
1
inconsistent assembly
month_released!
November, 2017
lab.title!
Bing Ren, UCSD
BIOSAMPLE
ASSAY
313 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
EndoC_BH1
15
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
HepG2
45
5
1
2
1
1
Panc1
13
1
1
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