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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
102
ChIP-seq
72
total RNA-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
DNase-seq
2
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
102
DNA binding
74
Transcription
12
DNA accessibility
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
82
recombinant protein
72
control
58
RNA binding protein
25
histone
25
histone modification
24
chromatin remodeller
13
broad histone mark
12
narrow histone mark
2
other context
2
other post-translational modification
Date released
74
November, 2017
65
February, 2021
29
August, 2021
16
October, 2019
January, 2019
6
February, 2023
4
March, 2020
4
November, 2018
2
December, 2018
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
170
bam
109
bigWig
80
fastq
75
tsv
38
bed narrowPeak
26
bigBed narrowPeak
15
bed broadPeak
15
bigBed broadPeak
15
tagAlign
2
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
1
vcf
Organism
201
Homo sapiens
Biosample type
2569
tissue
1017
primary cell
233
in vitro differentiated cells
205
cell line
9
stem cell
Organ
97
liver
62
artery
62
blood vessel
62
heart
62
vasculature
15
pancreas
8
embryo
6
blood
6
bodily fluid
4
kidney
3
epithelium
1
mammary gland
Project
198
AMP
5
T1D
2
community
Genome assembly (visualization)
118
hg19
99
GRCh38
Lab
177
AMP-T2D consortium
21
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
11
inconsistent control read length
assay_slims!
3D chromatin structure
audit.ERROR.category!
inconsistent ontology term
month_released!
January, 2019
target.investigated_as!
transcription factor
BIOSAMPLE
ASSAY
205 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
81
9
1
2
2
1
1
smooth muscle cell of the coronary artery
2
52
8
Panc1
13
1
H1-hESC
8
EndoC_BH1
3
2
1
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