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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
89
ChIP-seq
19
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
Hi-C
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
115
Transcription
89
DNA binding
19
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
83
control
9
transcription factor
3
histone
histone modification
3
nucleotide modification
2
RNA binding protein
2
broad histone mark
1
narrow histone mark
1
recombinant protein
Date released
82
February, 2021
64
November, 2017
29
August, 2021
20
May, 2021
14
October, 2019
10
March, 2020
8
January, 2019
6
November, 2020
5
November, 2018
4
February, 2023
3
November, 2019
2
March, 2023
1
December, 2018
1
January, 2018
1
May, 2020
1
October, 2022
Available data
547
bam
485
bigWig
411
fastq
bed narrowPeak
335
bigBed narrowPeak
119
tsv
45
bed broadPeak
45
bigBed broadPeak
9
tagAlign
3
bed bed3+
3
tar
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
247
Homo sapiens
Biosample type
1675
tissue
768
primary cell
251
cell line
221
in vitro differentiated cells
8
stem cell
Organ
90
liver
69
pancreas
63
epithelium
54
artery
54
blood vessel
54
heart
54
vasculature
11
kidney
8
embryo
7
blood
7
bodily fluid
1
mammary gland
Project
244
AMP
5
T1D
2
community
Genome assembly (visualization)
126
hg19
106
GRCh38
Lab
221
AMP-T2D consortium
19
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
3
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
70
inconsistent ontology term
Audit category:
1
missing controlled_by
Audit category:
1
inconsistent assembly
assay_title!
HiChIP
files.file_type!
bed narrowPeak
bedpe bed3+
target.investigated_as!
histone modification
BIOSAMPLE
ASSAY
251 results
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total RNA-seq
ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Capture-C
Hi-C
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
14
69
2
2
1
1
1
EndoC_BH1
33
2
18
6
3
2
1
smooth muscle cell of the coronary artery
52
2
H1-hESC
8
GM12878
6
1
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