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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
108
total RNA-seq
57
ChIP-seq
29
ATAC-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
DNase-seq
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
57
DNA binding
31
DNA accessibility
3
3D chromatin structure
1
DNA sequencing
Target of assay
24
transcription factor
22
histone
22
histone modification
21
control
11
broad histone mark
11
narrow histone mark
recombinant protein
3
nucleotide modification
2
RNA binding protein
Date released
96
February, 2021
44
August, 2021
23
October, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
493
bam
434
bigWig
fastq
316
bed narrowPeak
274
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
20
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
224
Homo sapiens
Biosample type
2360
tissue
679
primary cell
253
in vitro differentiated cells
228
cell line
6
stem cell
Organ
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
34
liver
12
kidney
8
embryo
1
blood
1
bodily fluid
1
mammary gland
Project
217
AMP
9
T1D
2
community
Genome assembly (visualization)
156
hg19
136
GRCh38
Lab
181
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
85
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
inconsistent assembly
files.file_type!
fastq
target.investigated_as!
recombinant protein
BIOSAMPLE
ASSAY
228 results
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total RNA-seq
ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
EndoC_BH1
33
15
19
6
3
1
2
2
1
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
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