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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
169
ChIP-seq
113
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
1
WGBS
1
whole genome sequencing assay
Assay category
169
DNA binding
113
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
120
transcription factor
31
RNA binding protein
27
control
23
histone
23
histone modification
23
recombinant protein
15
chromatin remodeller
12
narrow histone mark
11
broad histone mark
3
nucleotide modification
Date released
November, 2017
96
February, 2021
61
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
November, 2020
5
February, 2023
1
January, 2018
1
May, 2020
Available data
268
bam
254
bigWig
155
bed narrowPeak
119
tsv
112
fastq
106
bigBed narrowPeak
8
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bed broadPeak
1
bigBed bedMethyl
1
bigBed broadPeak
1
hdf5
1
vcf
Organism
343
Homo sapiens
Biosample type
2646
tissue
1079
primary cell
394
in vitro differentiated cells
343
cell line
8
stem cell
Organ
91
pancreas
86
liver
78
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
334
AMP
9
T1D
Genome assembly (visualization)
264
hg19
247
GRCh38
Lab
298
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Audit category:
92
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
BIOSAMPLE
ASSAY
343 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
WGBS
whole genome sequencing assay
cell line
HepG2
63
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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