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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
364
ChIP-seq
19
total RNA-seq
3
Hi-C
2
ATAC-seq
2
DNase-seq
2
STARR-seq
2
pCHi-C
1
RRBS
1
WGBS
1
whole genome sequencing assay
Assay category
364
DNA binding
19
Transcription
4
DNA accessibility
3
3D chromatin structure
2
DNA methylation
1
DNA sequencing
Target of assay
299
transcription factor
82
recombinant protein
62
control
56
RNA binding protein
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
300
November, 2017
46
November, 2018
29
August, 2021
5
December, 2019
5
January, 2019
3
December, 2017
2
February, 2021
2
July, 2019
2
June, 2019
1
December, 2018
1
May, 2020
1
October, 2019
Available data
363
bam
355
fastq
324
bigWig
297
bed narrowPeak
284
bigBed narrowPeak
46
bed broadPeak
46
bigBed broadPeak
20
tsv
4
bed bed3+
3
tar
2
bed bedMethyl
2
bigBed bedMethyl
2
tagAlign
1
bed bed3
1
bedpe bed3+
1
hdf5
1
hic
1
vcf
Organism
397
Homo sapiens
Biosample type
383
cell line
tissue
11
primary cell
3
in vitro differentiated cells
Organ
416
epithelium
397
liver
363
pancreas
92
connective tissue
86
vasculature
81
blood vessel
78
heart
68
artery
68
blood
68
bodily fluid
45
kidney
25
embryo
18
brain
7
vein
6
musculature of body
4
eye
3
adipose tissue
1
bone element
1
bone marrow
1
mammary gland
1
pericardium
Project
397
AMP
Genome assembly (visualization)
324
hg19
265
GRCh38
Lab
369
AMP-T2D consortium
28
Bing Ren, UCSD
Audit category:
1
inconsistent ontology term
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
target.investigated_as!
histone
biosample_type!
tissue
BIOSAMPLE
ASSAY
397 results
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ChIP-seq
total RNA-seq
Hi-C
ATAC-seq
DNase-seq
STARR-seq
pCHi-C
RRBS
WGBS
whole genome sequencing assay
cell line
HepG2
360
14
2
1
2
2
1
1
primary cell
hepatocyte
1
5
1
1
Liver fetal (hepatocyte)
1
endothelial cell of hepatic sinusoid
1
hepatic stellate cell
1
in vitro differentiated cells
hepatocyte
3
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