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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
341
total RNA-seq
150
ChIP-seq
109
ATAC-seq
11
DNase-seq
11
snATAC-seq
10
MeRIP-seq
6
Hi-C
5
pCHi-C
4
WGBS
2
Capture-C
2
FAIRE-seq
2
RRBS
2
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
Assay category
343
Transcription
150
DNA binding
133
DNA accessibility
6
3D chromatin structure
6
DNA methylation
Target of assay
95
histone
95
histone modification
51
broad histone mark
44
narrow histone mark
41
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
50
February, 2023
39
October, 2019
26
February, 2021
24
May, 2022
14
March, 2020
10
November, 2020
8
January, 2021
7
June, 2019
7
November, 2018
6
April, 2018
6
July, 2019
6
September, 2017
5
March, 2019
5
October, 2017
4
August, 2021
2
February, 2020
2
May, 2019
1
August, 2022
Available data
498
bam
434
bigWig
314
tsv
213
fastq
176
bed narrowPeak
72
bigBed narrowPeak
32
bed bed3+
24
bed broadPeak
19
tagAlign
10
bigBed broadPeak
6
bed bedMethyl
6
bigBed bedMethyl
6
txt
4
bedpe bed3+
4
hic
1
bedpe
1
hdf5
Organism
648
Homo sapiens
Biosample type
561
tissue
primary cell
92
cell line
3
in vitro differentiated cells
Organ
777
liver
645
connective tissue
600
pancreas
489
adipose tissue
340
heart
318
kidney
265
brain
199
blood vessel
199
vasculature
158
bone element
139
artery
122
limb
118
epithelium
82
musculature of body
61
blood
61
bodily fluid
56
eye
43
nerve
37
embryo
25
spleen
20
lung
18
ureter
16
skeleton
5
gonad
5
ovary
2
intestine
2
pituitary gland
2
thymus
1
adrenal gland
1
esophagus
1
large intestine
1
lymph node
1
mammary gland
1
pericardium
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
622
AMP
34
T1D
Genome assembly (visualization)
503
hg19
446
GRCh38
Lab
587
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
2
inconsistent assembly
biosample_type!
primary cell
BIOSAMPLE
ASSAY
656 results
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total RNA-seq
ChIP-seq
ATAC-seq
DNase-seq
snATAC-seq
MeRIP-seq
Hi-C
pCHi-C
WGBS
Capture-C
FAIRE-seq
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
tissue
islet of Langerhans
298
52
59
1
7
4
3
4
1
1
body of pancreas
3
35
4
4
2
2
pancreas
2
16
2
4
1
1
2
1
1
retina
3
15
3
endocrine pancreas
16
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cell line
EndoC_BH1
33
15
19
6
1
2
1
Panc1
13
1
1
in vitro differentiated cells
pancreatic PP cell
3
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