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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
395
ChIP-seq
33
total RNA-seq
2
ATAC-seq
2
DNase-seq
2
STARR-seq
2
pCHi-C
1
GRO-seq
1
RRBS
1
WGBS
1
whole genome sequencing assay
Assay category
395
DNA binding
33
Transcription
4
DNA accessibility
3D chromatin structure
2
DNA methylation
1
DNA sequencing
Target of assay
302
transcription factor
82
recombinant protein
69
control
56
RNA binding protein
45
histone
45
histone modification
narrow histone mark
21
broad histone mark
21
chromatin remodeller
2
other context
2
other post-translational modification
Date released
308
November, 2017
46
November, 2018
38
August, 2021
18
December, 2017
10
February, 2018
5
December, 2019
5
January, 2019
2
February, 2021
2
June, 2019
2
May, 2021
1
January, 2018
1
July, 2019
1
May, 2020
1
October, 2019
Available data
407
bam
388
fastq
362
bigWig
320
bed narrowPeak
298
bigBed narrowPeak
54
bed broadPeak
54
bigBed broadPeak
34
tsv
9
tagAlign
6
bed bed3+
3
tar
2
bed bedMethyl
2
bigBed bedMethyl
1
bed bed3
1
vcf
Organism
440
Homo sapiens
Biosample type
398
cell line
tissue
31
in vitro differentiated cells
11
primary cell
Organ
452
epithelium
411
liver
395
pancreas
116
connective tissue
91
vasculature
86
blood vessel
78
heart
68
artery
68
blood
68
bodily fluid
50
kidney
29
embryo
15
brain
14
vein
10
musculature of body
4
eye
3
adipose tissue
1
bone element
1
bone marrow
1
mammary gland
1
pericardium
Project
440
AMP
Genome assembly (visualization)
361
hg19
302
GRCh38
1
hg18
Lab
412
AMP-T2D consortium
28
Bing Ren, UCSD
Audit category:
5
inconsistent ontology term
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
23
inconsistent control read length
8
inconsistent control run_type
assay_slims!
3D chromatin structure
biosample_type!
tissue
target.investigated_as!
narrow histone mark
BIOSAMPLE
ASSAY
440 results
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ChIP-seq
total RNA-seq
ATAC-seq
DNase-seq
STARR-seq
pCHi-C
GRO-seq
RRBS
WGBS
whole genome sequencing assay
cell line
HepG2
369
14
1
2
2
1
1
H1-hESC
8
in vitro differentiated cells
pancreatic endoderm
12
4
1
hepatocyte
10
Hepatic endoderm
2
mesodermal cell (lineage marker-negative)
1
mesodermal cell (pacemaker intermediate)
1
primary cell
hepatocyte
2
5
1
1
Liver fetal (hepatocyte)
1
hepatic stellate cell
1
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