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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
99
total RNA-seq
46
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
6
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
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
Assay category
101
Transcription
46
DNA binding
30
DNA accessibility
2
3D chromatin structure
Target of assay
19
histone
19
histone modification
17
control
13
transcription factor
10
broad histone mark
9
narrow histone mark
7
recombinant protein
3
nucleotide modification
1
RNA binding protein
Date released
96
February, 2021
30
October, 2019
21
May, 2021
16
November, 2019
11
March, 2020
10
August, 2021
6
February, 2023
6
November, 2020
2
March, 2023
January, 2018
1
May, 2020
1
October, 2022
Available data
582
bam
507
bigWig
fastq
390
bed narrowPeak
355
bigBed narrowPeak
110
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
196
Homo sapiens
Biosample type
2394
tissue
679
primary cell
253
in vitro differentiated cells
200
cell line
6
stem cell
Organ
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
17
kidney
8
embryo
3
liver
1
mammary gland
Project
189
AMP
9
T1D
2
community
Genome assembly (visualization)
147
hg19
143
GRCh38
Lab
187
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
91
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
inconsistent assembly
month_released!
January, 2018
files.file_type!
fastq
lab.title!
Bing Ren, UCSD
BIOSAMPLE
ASSAY
200 results
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total RNA-seq
ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
cell line
EndoC_BH1
33
15
19
6
3
2
1
2
1
smooth muscle cell of the coronary artery
52
6
8
Panc1
13
1
1
H1-hESC
8
RCC 7860 HIF1a re-expression
1
4
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