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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
109
total RNA-seq
92
ChIP-seq
17
ATAC-seq
6
MeRIP-seq
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
HiChIP
2
pCHi-C
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
111
Transcription
92
DNA binding
17
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
83
control
9
transcription factor
3
histone
3
histone modification
3
nucleotide modification
2
RNA binding protein
2
broad histone mark
1
narrow histone mark
1
recombinant protein
Date released
82
February, 2021
66
November, 2017
30
August, 2021
20
May, 2021
15
October, 2019
March, 2020
8
January, 2019
6
February, 2023
6
November, 2020
5
November, 2018
4
November, 2019
2
March, 2023
1
December, 2018
1
January, 2018
1
May, 2020
1
October, 2022
Available data
577
bam
515
bigWig
427
fastq
bed narrowPeak
355
bigBed narrowPeak
110
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
244
Homo sapiens
Biosample type
1683
tissue
781
primary cell
254
in vitro differentiated cells
248
cell line
4
stem cell
Organ
93
liver
67
pancreas
60
epithelium
54
artery
54
blood vessel
54
heart
54
vasculature
9
kidney
8
embryo
7
blood
7
bodily fluid
Project
241
AMP
5
T1D
2
community
Genome assembly (visualization)
124
hg19
102
GRCh38
Lab
215
AMP-T2D consortium
20
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
65
inconsistent ontology term
Audit category:
1
missing controlled_by
Audit category:
2
inconsistent control read length
1
inconsistent assembly
files.file_type!
bed narrowPeak
month_released!
March, 2020
organ_slims!
brain
pericardium
BIOSAMPLE
ASSAY
248 results
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total RNA-seq
ChIP-seq
ATAC-seq
MeRIP-seq
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
pCHi-C
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
14
71
2
2
2
1
1
EndoC_BH1
31
2
16
6
1
3
2
2
1
smooth muscle cell of the coronary artery
52
2
H1-hESC
8
Panc1
7
1
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