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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
394
ChIP-seq
19
total RNA-seq
3
Hi-C
3
pCHi-C
2
ATAC-seq
2
DNase-seq
2
STARR-seq
1
RRBS
1
WGBS
1
whole genome sequencing assay
Assay category
394
DNA binding
19
Transcription
4
DNA accessibility
3
3D chromatin structure
2
DNA methylation
1
DNA sequencing
Target of assay
296
transcription factor
82
recombinant protein
62
control
55
RNA binding protein
33
histone
33
histone modification
21
chromatin remodeller
17
broad histone mark
16
narrow histone mark
2
other context
2
other post-translational modification
Date released
312
November, 2017
46
November, 2018
35
August, 2021
15
December, 2017
5
December, 2019
5
January, 2019
2
February, 2021
2
July, 2019
2
June, 2019
1
December, 2018
1
May, 2020
1
May, 2021
1
October, 2019
Available data
393
bam
382
fastq
357
bigWig
328
bed narrowPeak
309
bigBed narrowPeak
60
bed broadPeak
60
bigBed broadPeak
20
tsv
16
tagAlign
7
bed bed3+
tar
2
bed bedMethyl
2
bigBed bedMethyl
1
bed bed3
1
bedpe bed3+
1
hdf5
1
hic
1
vcf
Organism
428
Homo sapiens
Biosample type
398
cell line
tissue
15
in vitro differentiated cells
15
primary cell
Organ
508
epithelium
441
pancreas
427
liver
137
connective tissue
102
vasculature
96
blood vessel
80
heart
69
blood
69
bodily fluid
68
artery
55
kidney
37
embryo
21
brain
vein
14
musculature of body
5
eye
3
adipose tissue
1
bone element
1
bone marrow
1
mammary gland
1
pericardium
Project
427
AMP
1
T1D
Genome assembly (visualization)
354
hg19
293
GRCh38
Lab
396
AMP-T2D consortium
31
Bing Ren, UCSD
1
Kyle Gaulton, UCSD
Audit category:
1
inconsistent ontology term
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
biosample_type!
tissue
files.file_type!
tar
organ_slims!
vein
BIOSAMPLE
ASSAY
428 results
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ChIP-seq
total RNA-seq
Hi-C
pCHi-C
ATAC-seq
DNase-seq
STARR-seq
RRBS
WGBS
whole genome sequencing assay
cell line
HepG2
375
14
2
2
1
2
1
1
in vitro differentiated cells
hepatocyte
15
primary cell
hepatocyte
4
5
1
1
Liver fetal (hepatocyte)
1
endothelial cell of hepatic sinusoid
1
hepatic stellate cell
1
megakaryocyte
1
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