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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
276
total RNA-seq
153
ChIP-seq
28
ATAC-seq
8
DNase-seq
8
single cell RNA-seq
4
WGBS
3
Hi-C
2
FAIRE-seq
2
RRBS
2
small RNA-seq
1
pCHi-C
1
snATAC-seq
Assay category
286
Transcription
153
DNA binding
39
DNA accessibility
6
DNA methylation
3
3D chromatin structure
Target of assay
103
histone
103
histone modification
56
broad histone mark
47
narrow histone mark
33
control
17
transcription factor
8
RNA binding protein
Date released
159
August, 2017
126
July, 2018
51
October, 2018
39
November, 2019
36
May, 2021
18
October, 2019
11
September, 2018
9
March, 2020
8
April, 2018
7
November, 2018
6
July, 2019
6
September, 2017
4
June, 2019
4
October, 2017
2
May, 2019
1
August, 2022
1
February, 2020
Available data
449
bam
411
bigWig
282
tsv
217
fastq
123
bed narrowPeak
69
bigBed narrowPeak
29
bed bed3+
19
bed broadPeak
16
tagAlign
7
bigBed broadPeak
6
bed bedMethyl
6
bigBed bedMethyl
2
bedpe bed3+
2
hic
1
hdf5
Organism
481
Homo sapiens
Biosample type
442
tissue
31
primary cell
15
cell line
Organ
725
pancreas
720
liver
679
connective tissue
491
adipose tissue
epithelium
353
heart
286
brain
236
vasculature
230
blood vessel
163
kidney
158
bone element
141
artery
122
limb
96
musculature of body
61
blood
61
bodily fluid
61
eye
43
nerve
37
embryo
25
spleen
22
vein
18
ureter
16
skeleton
5
gonad
5
ovary
2
intestine
2
pericardium
2
pituitary gland
1
adrenal gland
1
esophagus
1
large intestine
1
lung
1
lymph node
1
mammary gland
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
thymus
1
urinary bladder
Project
484
AMP
4
T1D
Genome assembly (visualization)
430
hg19
422
GRCh38
Lab
488
AMP-T2D consortium
51
Kyle Gaulton, UCSD
4
Bing Ren, UCSD
4
Rohit N. Kulkarni, M.D., Ph.D.
Mark McCarthy, Oxford
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
organ_slims!
epithelium
lab.title!
Mark McCarthy, Oxford
BIOSAMPLE
ASSAY
488 results
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total RNA-seq
ChIP-seq
ATAC-seq
DNase-seq
single cell RNA-seq
WGBS
Hi-C
FAIRE-seq
RRBS
small RNA-seq
pCHi-C
snATAC-seq
tissue
islet of Langerhans
272
50
24
1
1
1
1
1
body of pancreas
3
35
4
4
2
2
pancreas
1
16
2
2
1
1
1
1
endocrine pancreas
16
primary cell
pancreatic endocrine cell
23
pancreatic stellate cell
4
co-expressing pancreatic endocrine cell
2
unclassified pancreatic endocrine cell
2
cell line
Panc1
13
1
1
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