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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
477
ChIP-seq
19
ATAC-seq
6
MeRIP-seq
5
STARR-seq
4
Hi-C
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
pCHi-C
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
477
DNA binding
21
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
357
transcription factor
89
recombinant protein
81
control
65
RNA binding protein
37
histone
37
histone modification
30
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
18
January, 2019
17
May, 2021
15
November, 2019
6
November, 2020
4
February, 2021
3
February, 2023
March, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
511
bam
459
bigWig
427
fastq
391
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
tsv
14
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
520
Homo sapiens
Biosample type
1620
tissue
817
primary cell
524
cell line
259
in vitro differentiated cells
6
stem cell
Organ
386
liver
61
blood
61
bodily fluid
56
pancreas
42
epithelium
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
519
AMP
3
T1D
2
community
Genome assembly (visualization)
411
hg19
347
GRCh38
Lab
489
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
2
Kyle Gaulton, UCSD
Audit category:
51
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
1
inconsistent assembly
assay_title!
CRISPR genome editing followed by DNA sequencing
files.file_type!
tsv
month_released!
March, 2020
organ_slims!
artery
BIOSAMPLE
ASSAY
524 results
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ChIP-seq
ATAC-seq
MeRIP-seq
STARR-seq
Hi-C
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
pCHi-C
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
1
2
2
1
1
1
GM12878
60
1
EndoC_BH1
14
17
6
1
2
2
1
Panc1
13
1
1
RCC 7860 HIF1a re-expression
4
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