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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
283
total RNA-seq
120
ChIP-seq
60
ATAC-seq
14
single cell RNA-seq
11
snATAC-seq
5
Hi-C
4
WGBS
2
FAIRE-seq
2
MeRIP-seq
2
RRBS
2
small RNA-seq
1
DNase-seq
1
pCHi-C
Assay category
299
Transcription
120
DNA binding
74
DNA accessibility
6
DNA methylation
5
3D chromatin structure
Target of assay
103
histone
103
histone modification
56
broad histone mark
47
narrow histone mark
control
17
transcription factor
8
RNA binding protein
2
nucleotide modification
Date released
150
August, 2017
126
July, 2018
40
October, 2018
39
November, 2019
37
May, 2021
24
May, 2022
18
February, 2023
11
October, 2019
11
September, 2018
9
March, 2020
8
April, 2018
8
January, 2021
6
July, 2019
5
November, 2018
5
October, 2017
3
March, 2019
2
August, 2021
2
November, 2020
1
August, 2022
1
February, 2020
1
May, 2019
Available data
446
bam
412
bigWig
283
tsv
224
fastq
141
bed narrowPeak
69
bigBed narrowPeak
27
bed bed3+
20
bed broadPeak
14
tagAlign
bigBed broadPeak
6
bed bedMethyl
6
bigBed bedMethyl
6
txt
3
bedpe bed3+
3
hic
1
bedpe
1
hdf5
Organism
501
Homo sapiens
Biosample type
468
tissue
31
primary cell
8
cell line
Organ
884
pancreas
640
connective tissue
620
liver
epithelium
465
adipose tissue
343
heart
264
kidney
217
brain
197
vasculature
196
blood vessel
159
bone element
128
artery
69
limb
63
blood
63
bodily fluid
57
musculature of body
56
eye
30
embryo
30
nerve
20
lung
16
skeleton
16
spleen
16
vein
5
gonad
5
ovary
2
intestine
2
pericardium
2
pituitary gland
2
thymus
1
adrenal gland
1
bone marrow
1
esophagus
1
large intestine
1
lymph node
1
mammary gland
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
477
AMP
30
T1D
Genome assembly (visualization)
444
hg19
415
GRCh38
Lab
448
AMP-T2D consortium
51
Kyle Gaulton, UCSD
4
Bing Ren, UCSD
Mark McCarthy, Oxford
2
Rohit N. Kulkarni, M.D., Ph.D.
1
Maike Sander, UCSD
1
Stephen Parker, UMich
Audit category:
4
inconsistent ontology term
1
audit script error
Audit category:
33
missing controlled_by
Audit category:
5
inconsistent control read length
2
inconsistent assembly
files.file_type!
bigBed broadPeak
lab.title!
Mark McCarthy, Oxford
organ_slims!
epithelium
target.investigated_as!
control
BIOSAMPLE
ASSAY
507 results
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total RNA-seq
ChIP-seq
ATAC-seq
single cell RNA-seq
snATAC-seq
Hi-C
WGBS
FAIRE-seq
MeRIP-seq
RRBS
small RNA-seq
DNase-seq
pCHi-C
tissue
islet of Langerhans
278
37
56
6
7
3
1
2
1
1
body of pancreas
3
26
4
2
2
pancreas
2
13
4
1
2
1
1
1
endocrine pancreas
14
primary cell
pancreatic endocrine cell
23
pancreatic stellate cell
4
co-expressing pancreatic endocrine cell
2
unclassified pancreatic endocrine cell
2
cell line
Panc1
7
1
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