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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
64
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
DNase-seq
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
pCHi-C
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
64
DNA binding
30
DNA accessibility
3
3D chromatin structure
2
Transcription
1
DNA sequencing
Target of assay
24
transcription factor
22
histone
22
histone modification
21
control
11
broad histone mark
11
narrow histone mark
7
recombinant protein
3
nucleotide modification
2
RNA binding protein
Date released
27
August, 2021
26
October, 2019
18
February, 2021
17
May, 2021
15
November, 2019
6
November, 2020
4
February, 2023
2
March, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
582
bam
522
bigWig
fastq
404
bed narrowPeak
355
bigBed narrowPeak
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
115
Homo sapiens
Biosample type
1421
tissue
383
primary cell
137
in vitro differentiated cells
119
cell line
2
stem cell
Organ
58
pancreas
44
epithelium
24
liver
14
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
1
blood
1
bodily fluid
Project
112
AMP
5
T1D
2
community
Genome assembly (visualization)
63
hg19
44
GRCh38
Lab
83
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
3
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
53
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
inconsistent assembly
assay_title!
HiChIP
files.file_type!
fastq
tsv
zippedFastqFolder
BIOSAMPLE
ASSAY
119 results
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ChIP-seq
ATAC-seq
MeRIP-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
pCHi-C
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
EndoC_BH1
15
18
6
3
1
2
1
HepG2
18
1
2
1
1
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
RCC 7860 HIF1a re-expression
4
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