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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
113
total RNA-seq
109
ChIP-seq
29
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
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
115
Transcription
109
DNA binding
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
89
recombinant protein
83
control
61
RNA binding protein
26
chromatin remodeller
24
histone
24
histone modification
13
narrow histone mark
11
broad histone mark
3
nucleotide modification
1
other context
1
other post-translational modification
Date released
91
February, 2021
60
November, 2017
33
August, 2021
22
October, 2019
21
May, 2021
15
November, 2019
11
March, 2020
9
January, 2019
6
February, 2023
6
November, 2020
4
November, 2018
3
December, 2018
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
233
bam
166
bigWig
119
tsv
90
fastq
52
bed narrowPeak
27
bigBed narrowPeak
15
bed broadPeak
bigBed broadPeak
15
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
282
Homo sapiens
Biosample type
2472
tissue
1034
primary cell
344
in vitro differentiated cells
286
cell line
10
stem cell
Organ
90
liver
90
pancreas
78
epithelium
62
artery
62
blood vessel
62
heart
62
vasculature
12
kidney
10
blood
10
bodily fluid
8
embryo
1
mammary gland
Project
275
AMP
9
T1D
2
community
Genome assembly (visualization)
163
hg19
142
GRCh38
Lab
250
AMP-T2D consortium
23
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
84
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
1
inconsistent assembly
files.file_type!
bigBed broadPeak
target.investigated_as!
transcription factor
BIOSAMPLE
ASSAY
286 results
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Clear Filters
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
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
14
67
1
2
2
2
1
1
EndoC_BH1
33
14
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
52
2
8
Panc1
13
1
GM12878
9
1
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