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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
446
ChIP-seq
68
total RNA-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
Hi-C
2
HiChIP
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
446
DNA binding
70
Transcription
10
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
353
transcription factor
82
recombinant protein
69
control
64
RNA binding protein
30
chromatin remodeller
19
histone
19
histone modification
10
narrow histone mark
9
broad histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
61
November, 2018
33
August, 2021
28
December, 2018
23
January, 2019
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
496
bam
446
bigWig
427
fastq
375
bed narrowPeak
347
bigBed narrowPeak
71
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hic
1
txt
1
vcf
Organism
541
Homo sapiens
Biosample type
2446
tissue
1002
primary cell
545
cell line
254
in vitro differentiated cells
9
stem cell
Organ
401
liver
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
embryo
2
kidney
1
epithelium
1
mammary gland
1
pancreas
Project
538
AMP
5
T1D
2
community
Genome assembly (visualization)
452
hg19
389
GRCh38
Lab
505
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
audit.ERROR.category!
inconsistent ontology term
organ_slims!
embryo
month_released!
October, 2019
BIOSAMPLE
ASSAY
545 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
EndoC_BH1
3
2
1
EndoC-BH1
1
1
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