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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
9
total RNA-seq
6
MeRIP-seq
6
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
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
138
DNA binding
DNA accessibility
10
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
10
October, 2019
6
February, 2023
6
November, 2020
4
February, 2021
4
March, 2020
4
November, 2018
3
January, 2019
3
November, 2019
1
December, 2018
1
March, 2023
1
May, 2020
1
October, 2022
Available data
119
bam
106
fastq
65
bigWig
46
bed narrowPeak
32
bigBed narrowPeak
14
bed broadPeak
14
bigBed broadPeak
14
tsv
6
tagAlign
3
tar
2
bedpe bed3+
2
hic
1
bed bed3+
1
txt
1
vcf
Organism
175
Homo sapiens
Biosample type
783
tissue
340
primary cell
178
cell line
104
in vitro differentiated cells
7
stem cell
Organ
133
liver
19
pancreas
12
epithelium
7
kidney
6
blood
6
bodily fluid
2
artery
2
blood vessel
2
heart
2
vasculature
1
mammary gland
Project
172
AMP
5
T1D
1
community
Genome assembly (visualization)
515
hg19
GRCh38
Lab
132
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
1
Anna Gloyn, Oxford
Audit category:
17
inconsistent ontology term
Audit category:
8
missing controlled_by
Audit category:
4
inconsistent control read length
2
inconsistent control run_type
assay_slims!
DNA accessibility
assay_title!
siRNA RNA-seq
assembly!
GRCh38
BIOSAMPLE
ASSAY
178 results
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ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
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
whole genome sequencing assay
cell line
HepG2
117
9
2
2
2
1
EndoC_BH1
2
6
3
1
2
2
1
Panc1
7
GM12878
6
HEK293T
2
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