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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
478
ChIP-seq
20
ATAC-seq
6
MeRIP-seq
5
STARR-seq
4
Hi-C
3
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
478
DNA binding
22
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
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
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
February, 2023
6
November, 2020
4
February, 2021
2
March, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
516
bam
466
bigWig
427
fastq
392
bed narrowPeak
355
bigBed narrowPeak
tsv
59
bed broadPeak
59
bigBed broadPeak
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
525
Homo sapiens
Biosample type
1632
tissue
818
primary cell
529
cell line
263
in vitro differentiated cells
6
stem cell
Organ
386
liver
61
blood
61
bodily fluid
58
pancreas
44
epithelium
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
520
AMP
7
T1D
2
community
Genome assembly (visualization)
413
hg19
348
GRCh38
Lab
491
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
53
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
organ_slims!
artery
files.file_type!
tsv
BIOSAMPLE
ASSAY
529 results
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Clear Filters
ChIP-seq
ATAC-seq
MeRIP-seq
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
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
15
18
6
1
3
2
2
1
Panc1
13
1
1
RCC 7860 HIF1a re-expression
4
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