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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
72
total RNA-seq
39
ChIP-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
DNase-seq
2
Hi-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
74
Transcription
39
DNA binding
12
DNA accessibility
2
3D chromatin structure
1
DNA sequencing
Target of assay
16
transcription factor
13
control
10
histone
10
histone modification
5
broad histone mark
5
narrow histone mark
1
RNA binding protein
Date released
70
February, 2021
41
August, 2021
17
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
520
bam
464
bigWig
fastq
383
bed narrowPeak
355
bigBed narrowPeak
80
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
139
Homo sapiens
Biosample type
2295
tissue
625
primary cell
143
cell line
142
in vitro differentiated cells
5
stem cell
Organ
66
artery
66
blood vessel
66
heart
66
vasculature
34
liver
16
pancreas
8
embryo
4
kidney
3
epithelium
1
blood
1
bodily fluid
1
mammary gland
Project
136
AMP
5
T1D
2
community
Genome assembly (visualization)
103
hg19
86
GRCh38
Lab
103
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
files.file_type!
bigBed bedMethyl
fastq
BIOSAMPLE
ASSAY
143 results
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Clear Filters
total RNA-seq
ChIP-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
DNase-seq
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
smooth muscle cell of the coronary artery
52
6
8
HepG2
9
18
1
2
2
1
1
Panc1
13
1
1
H1-hESC
8
EndoC_BH1
3
2
1
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