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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
129
ChIP-seq
19
ATAC-seq
9
total RNA-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
Hi-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
129
DNA binding
19
DNA accessibility
11
Transcription
2
3D chromatin structure
1
DNA sequencing
Target of assay
81
control
52
transcription factor
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
92
November, 2017
35
August, 2021
16
May, 2021
10
October, 2019
6
February, 2023
6
March, 2020
6
November, 2020
4
February, 2021
4
November, 2018
3
January, 2019
November, 2019
2
March, 2023
1
December, 2018
1
January, 2018
1
May, 2020
1
October, 2022
Available data
111
bam
100
fastq
63
bigWig
41
bed narrowPeak
28
bigBed narrowPeak
15
tsv
13
bed broadPeak
13
bigBed broadPeak
6
tagAlign
2
tar
1
bed bed3+
1
bedpe bed3+
1
hic
1
txt
1
vcf
Organism
184
Homo sapiens
Biosample type
916
tissue
543
primary cell
188
cell line
124
in vitro differentiated cells
7
stem cell
Organ
126
liver
34
pancreas
27
epithelium
7
blood
7
bodily fluid
7
kidney
2
artery
2
blood vessel
2
heart
2
vasculature
1
mammary gland
Project
181
AMP
5
T1D
2
community
Genome assembly (visualization)
455
hg19
GRCh38
Lab
142
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
32
inconsistent ontology term
Audit category:
7
missing controlled_by
Audit category:
3
inconsistent control read length
1
inconsistent control run_type
assembly!
GRCh38
month_released!
June, 2019
November, 2019
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
188 results
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ChIP-seq
ATAC-seq
total RNA-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Capture-C
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
110
9
2
2
2
1
EndoC_BH1
18
6
3
2
2
1
GM12878
6
1
Panc1
7
EndoC-BH1
1
1
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