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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
316
total RNA-seq
89
ChIP-seq
81
ATAC-seq
11
snATAC-seq
10
MeRIP-seq
6
Hi-C
6
single cell RNA-seq
4
WGBS
2
Capture-C
2
RRBS
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
pCHi-C
Assay category
322
Transcription
92
DNA accessibility
89
DNA binding
6
3D chromatin structure
6
DNA methylation
Target of assay
44
histone
44
histone modification
41
control
23
narrow histone mark
21
broad histone mark
9
transcription factor
5
nucleotide modification
3
RNA binding protein
Date released
133
August, 2017
120
July, 2018
61
May, 2021
55
November, 2019
26
February, 2021
24
May, 2022
19
February, 2023
14
March, 2020
11
October, 2018
11
October, 2019
10
November, 2020
8
January, 2021
6
April, 2018
6
September, 2017
5
March, 2019
5
October, 2017
4
August, 2021
4
July, 2019
4
November, 2018
1
August, 2022
1
February, 2020
1
May, 2019
Available data
493
bam
429
bigWig
307
tsv
213
fastq
146
bed narrowPeak
bigBed narrowPeak
29
bed bed3+
21
bed broadPeak
19
tagAlign
7
bigBed broadPeak
6
bed bedMethyl
6
bigBed bedMethyl
6
txt
4
bedpe bed3+
4
hic
1
bedpe
1
hdf5
Organism
527
Homo sapiens
Biosample type
441
tissue
primary cell
85
cell line
3
in vitro differentiated cells
Organ
630
connective tissue
529
pancreas
477
adipose tissue
417
liver
291
heart
224
kidney
158
bone element
145
brain
137
blood vessel
137
vasculature
114
artery
103
epithelium
53
eye
43
musculature of body
38
limb
37
embryo
20
lung
17
nerve
16
skeleton
12
spleen
7
blood
7
bodily fluid
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
495
AMP
34
T1D
Genome assembly (visualization)
404
hg19
374
GRCh38
Lab
460
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:
1
inconsistent assembly
assay_title!
small RNA-seq
biosample_type!
primary cell
files.file_type!
bigBed narrowPeak
csv
BIOSAMPLE
ASSAY
529 results
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total RNA-seq
ChIP-seq
ATAC-seq
snATAC-seq
MeRIP-seq
Hi-C
single cell RNA-seq
WGBS
Capture-C
RRBS
CRISPR genome editing followed by sgRNA sequencing
pCHi-C
tissue
islet of Langerhans
278
50
58
7
4
3
6
1
body of pancreas
3
9
4
2
pancreas
2
3
4
1
2
1
1
endocrine pancreas
2
cell line
EndoC_BH1
33
15
19
6
1
2
1
Panc1
7
1
in vitro differentiated cells
pancreatic PP cell
3
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