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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
72
ChIP-seq
26
ATAC-seq
9
total RNA-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
HiChIP
1
whole genome sequencing assay
Assay category
72
DNA binding
26
DNA accessibility
9
Transcription
3
3D chromatin structure
1
DNA sequencing
Target of assay
70
control
4
transcription factor
3
nucleotide modification
2
RNA binding protein
1
broad histone mark
1
histone
1
histone modification
Date released
47
November, 2017
22
August, 2021
16
May, 2021
13
February, 2021
10
October, 2019
6
November, 2020
5
February, 2023
4
March, 2020
4
November, 2019
3
January, 2019
3
November, 2018
1
December, 2018
1
May, 2020
Available data
569
bam
bigWig
414
fastq
392
bed narrowPeak
343
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
vcf
Organism
135
Homo sapiens
Biosample type
1001
tissue
475
primary cell
135
cell line
134
in vitro differentiated cells
5
stem cell
Organ
68
liver
35
pancreas
28
epithelium
10
artery
10
blood vessel
10
heart
10
vasculature
7
kidney
6
blood
6
bodily fluid
1
mammary gland
Project
130
AMP
5
T1D
Genome assembly (visualization)
13
hg19
10
GRCh38
Lab
104
AMP-T2D consortium
20
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Audit category:
34
inconsistent ontology term
1
inconsistent replicate
Audit category:
missing controlled_by
files.file_type!
bigWig
audit.NOT_COMPLIANT.category!
missing controlled_by
BIOSAMPLE
ASSAY
135 results
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ChIP-seq
ATAC-seq
total RNA-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
HiChIP
whole genome sequencing assay
cell line
HepG2
51
1
9
2
2
2
1
EndoC_BH1
2
17
6
3
1
2
2
smooth muscle cell of the coronary artery
2
8
Panc1
7
GM12878
6
HEK293T
2
RCC 7860 vector
1
1
MCF-7
1
RCC 7860 HIF1a re-expression
1
RCC 7860 HIF2a over-expression
1
RCC 7860 VHL
1
Synthesized DNA
1
fibroblast cell line
1
iPSC derived cell line
1
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