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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
108
total RNA-seq
19
ATAC-seq
18
ChIP-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-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
110
Transcription
19
DNA accessibility
18
DNA binding
3
3D chromatin structure
1
DNA sequencing
Target of assay
21
control
3
nucleotide modification
1
broad histone mark
1
histone
histone modification
Date released
82
February, 2021
30
August, 2021
20
May, 2021
14
October, 2019
10
March, 2020
6
February, 2023
6
November, 2020
4
November, 2019
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
547
bam
485
bigWig
fastq
bed narrowPeak
335
bigBed narrowPeak
119
tsv
45
bed broadPeak
45
bigBed broadPeak
9
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
173
Homo sapiens
Biosample type
1481
tissue
464
primary cell
181
in vitro differentiated cells
177
cell line
6
stem cell
Organ
70
pancreas
64
epithelium
54
artery
54
blood vessel
54
heart
54
vasculature
19
liver
11
kidney
8
embryo
1
blood
1
bodily fluid
1
mammary gland
Project
168
AMP
7
T1D
2
community
Genome assembly (visualization)
106
hg19
100
GRCh38
Lab
144
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
inconsistent assembly
files.file_type!
bed narrowPeak
fastq
target.investigated_as!
histone modification
BIOSAMPLE
ASSAY
177 results
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total RNA-seq
ATAC-seq
ChIP-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
EndoC_BH1
33
18
2
6
3
1
2
2
1
smooth muscle cell of the coronary artery
52
2
HepG2
9
4
2
2
1
1
H1-hESC
8
Panc1
6
1
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