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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
113
total RNA-seq
86
ChIP-seq
18
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
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
115
Transcription
86
DNA binding
18
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
79
control
9
transcription factor
3
nucleotide modification
2
RNA binding protein
1
broad histone mark
1
histone
1
histone modification
1
recombinant protein
Date released
79
February, 2021
63
November, 2017
30
August, 2021
20
May, 2021
15
October, 2019
10
March, 2020
8
January, 2019
6
February, 2023
6
November, 2020
5
November, 2018
4
November, 2019
2
March, 2023
1
December, 2018
January, 2018
1
May, 2020
Available data
582
bam
521
bigWig
427
fastq
bed narrowPeak
355
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
txt
1
vcf
Organism
247
Homo sapiens
Biosample type
1541
tissue
791
primary cell
250
cell line
235
in vitro differentiated cells
7
stem cell
Organ
90
liver
71
pancreas
64
epithelium
52
artery
52
blood vessel
52
heart
52
vasculature
11
kidney
8
embryo
6
blood
6
bodily fluid
1
mammary gland
Project
241
AMP
7
T1D
2
community
Genome assembly (visualization)
126
hg19
106
GRCh38
Lab
217
AMP-T2D consortium
20
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
71
inconsistent ontology term
Audit category:
1
missing controlled_by
Audit category:
1
inconsistent assembly
files.file_type!
bed narrowPeak
tagAlign
txt
month_released!
January, 2018
BIOSAMPLE
ASSAY
250 results
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total RNA-seq
ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
14
68
2
2
2
1
1
EndoC_BH1
33
2
18
6
1
3
2
2
1
smooth muscle cell of the coronary artery
52
H1-hESC
8
Panc1
7
1
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