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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
total RNA-seq
92
ChIP-seq
19
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
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
92
DNA binding
19
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
83
control
9
transcription factor
3
histone
3
histone modification
3
nucleotide modification
2
RNA binding protein
2
broad histone mark
1
narrow histone mark
1
recombinant protein
Date released
66
November, 2017
16
May, 2021
13
August, 2021
11
October, 2019
6
March, 2020
6
November, 2020
5
February, 2023
5
November, 2018
4
February, 2021
3
January, 2019
3
November, 2019
2
March, 2023
1
December, 2018
1
January, 2018
1
May, 2020
1
October, 2022
Available data
478
bam
422
fastq
418
bigWig
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
tsv
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
141
Homo sapiens
Biosample type
762
tissue
546
primary cell
144
cell line
126
in vitro differentiated cells
8
stem cell
Organ
79
liver
37
pancreas
29
epithelium
7
blood
7
bodily fluid
7
kidney
2
artery
2
blood vessel
2
heart
2
vasculature
1
mammary gland
Project
137
AMP
5
T1D
2
community
Genome assembly (visualization)
26
hg19
2
GRCh38
Lab
120
AMP-T2D consortium
11
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
35
inconsistent ontology term
Audit category:
1
missing controlled_by
Audit category:
2
inconsistent control read length
1
inconsistent assembly
assay_title!
CRISPR genome editing followed by sgRNA sequencing
total RNA-seq
files.file_type!
bed narrowPeak
BIOSAMPLE
ASSAY
144 results
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ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
71
2
2
2
1
1
EndoC_BH1
2
18
6
1
3
2
2
Panc1
7
1
GM12878
6
1
EndoC-BH1
1
1
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