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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
138
ChIP-seq
19
ATAC-seq
9
total RNA-seq
6
MeRIP-seq
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
138
DNA binding
19
DNA accessibility
11
Transcription
3
3D chromatin structure
1
DNA sequencing
Target of assay
83
control
52
transcription factor
7
RNA binding protein
6
histone
6
histone modification
3
broad histone mark
3
narrow histone mark
3
nucleotide modification
2
chromatin remodeller
1
recombinant protein
Date released
98
November, 2017
36
August, 2021
16
May, 2021
10
October, 2019
6
February, 2023
6
November, 2020
4
November, 2018
3
February, 2021
3
January, 2019
3
November, 2019
2
March, 2020
2
March, 2023
1
December, 2018
1
January, 2018
1
October, 2022
Available data
119
bam
106
fastq
68
bigWig
46
bed narrowPeak
32
bigBed narrowPeak
14
bed broadPeak
14
bigBed broadPeak
10
tsv
6
tagAlign
3
tar
2
bedpe bed3+
2
hic
1
txt
1
vcf
Organism
188
Homo sapiens
Biosample type
893
tissue
535
primary cell
192
cell line
124
in vitro differentiated cells
3
stem cell
Organ
131
liver
37
pancreas
30
epithelium
7
blood
7
bodily fluid
5
kidney
2
artery
2
blood vessel
2
heart
2
vasculature
Project
185
AMP
5
T1D
2
community
Genome assembly (visualization)
529
hg19
GRCh38
Lab
145
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
33
inconsistent ontology term
Audit category:
8
missing controlled_by
Audit category:
4
inconsistent control read length
2
inconsistent control run_type
assay_title!
pCHi-C
assembly!
GRCh38
BIOSAMPLE
ASSAY
192 results
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ChIP-seq
ATAC-seq
total RNA-seq
MeRIP-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
117
9
2
2
1
EndoC_BH1
2
18
6
3
1
2
2
1
GM12878
6
1
Panc1
7
EndoC-BH1
1
1
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