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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
322
total RNA-seq
135
ChIP-seq
78
ATAC-seq
11
snATAC-seq
10
MeRIP-seq
7
DNase-seq
5
Hi-C
4
WGBS
2
Capture-C
2
FAIRE-seq
2
RRBS
2
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
pCHi-C
Assay category
324
Transcription
135
DNA binding
98
DNA accessibility
6
DNA methylation
5
3D chromatin structure
Target of assay
86
histone
86
histone modification
47
broad histone mark
39
narrow histone mark
35
control
19
transcription factor
9
RNA binding protein
5
nucleotide modification
Date released
147
August, 2017
120
July, 2018
61
May, 2021
55
November, 2019
51
October, 2018
26
February, 2021
24
May, 2022
19
February, 2023
October, 2019
14
March, 2020
10
November, 2020
8
January, 2021
7
November, 2018
6
April, 2018
6
July, 2019
6
September, 2017
5
March, 2019
5
October, 2017
4
August, 2021
4
June, 2019
2
May, 2019
1
August, 2022
1
February, 2020
Available data
481
bam
423
bigWig
309
tsv
213
fastq
139
bed narrowPeak
62
bigBed narrowPeak
27
bed bed3+
20
bed broadPeak
19
tagAlign
6
bed bedMethyl
6
bigBed bedMethyl
6
bigBed broadPeak
6
txt
4
bedpe bed3+
4
hic
1
bedpe
Organism
574
Homo sapiens
Biosample type
502
tissue
primary cell
77
cell line
3
in vitro differentiated cells
Organ
771
liver
641
connective tissue
582
pancreas
488
adipose tissue
332
heart
179
brain
173
blood vessel
173
vasculature
158
bone element
157
kidney
116
epithelium
113
artery
82
musculature of body
61
blood
61
bodily fluid
53
limb
37
embryo
35
eye
25
spleen
20
lung
18
ureter
16
skeleton
2
intestine
2
thymus
1
adrenal gland
1
esophagus
1
gonad
1
large intestine
1
mammary gland
1
nerve
1
ovary
1
pericardium
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
548
AMP
34
T1D
Genome assembly (visualization)
465
hg19
435
GRCh38
Lab
513
AMP-T2D consortium
51
Kyle Gaulton, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
4
Bing Ren, UCSD
2
Mark McCarthy, Oxford
1
Maike Sander, UCSD
1
Stephen Parker, UMich
Audit category:
76
inconsistent ontology term
1
audit script error
Audit category:
10
missing controlled_by
Audit category:
5
inconsistent control read length
1
inconsistent assembly
lab.title!
Katalin Susztak, Upenn
month_released!
October, 2019
biosample_type!
primary cell
BIOSAMPLE
ASSAY
582 results
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total RNA-seq
ChIP-seq
ATAC-seq
snATAC-seq
MeRIP-seq
DNase-seq
Hi-C
WGBS
Capture-C
FAIRE-seq
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
pCHi-C
tissue
islet of Langerhans
284
50
55
7
4
1
3
1
1
body of pancreas
3
35
4
4
2
2
pancreas
2
16
4
2
1
2
1
1
1
endocrine pancreas
16
cell line
EndoC_BH1
33
15
19
6
1
2
1
in vitro differentiated cells
pancreatic PP cell
3
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