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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
212
total RNA-seq
71
ChIP-seq
43
ATAC-seq
5
DNase-seq
4
Hi-C
2
Capture-C
2
RRBS
2
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
pCHi-C
1
snATAC-seq
Assay category
214
Transcription
71
DNA binding
49
DNA accessibility
4
3D chromatin structure
2
DNA methylation
Target of assay
51
histone
51
histone modification
26
broad histone mark
25
narrow histone mark
18
control
2
transcription factor
1
RNA binding protein
Date released
118
July, 2018
60
May, 2021
55
November, 2019
26
February, 2021
20
August, 2017
18
October, 2019
16
October, 2018
14
March, 2020
6
July, 2019
4
June, 2019
2
August, 2021
2
May, 2019
1
August, 2022
1
February, 2020
1
February, 2023
Available data
470
bam
430
bigWig
308
tsv
fastq
128
bed narrowPeak
69
bigBed narrowPeak
29
bed bed3+
19
bed broadPeak
19
tagAlign
7
bigBed broadPeak
6
bed bedMethyl
6
bigBed bedMethyl
3
bedpe bed3+
3
hic
1
hdf5
Organism
343
Homo sapiens
Biosample type
255
tissue
86
cell line
primary cell
3
in vitro differentiated cells
Organ
543
connective tissue
445
adipose tissue
344
pancreas
340
heart
253
brain
241
liver
199
blood vessel
199
vasculature
158
bone element
139
artery
127
kidney
122
limb
93
epithelium
80
musculature of body
56
eye
43
nerve
18
ureter
16
skeleton
10
embryo
5
gonad
5
ovary
2
intestine
2
pituitary gland
1
adrenal gland
1
blood
1
bodily fluid
1
esophagus
1
large intestine
1
lung
1
lymph node
1
mammary gland
1
pericardium
1
skin of body
1
small intestine
1
spinal cord
1
spleen
1
stomach
1
thymus
1
urinary bladder
Project
336
AMP
8
T1D
Genome assembly (visualization)
284
hg19
271
GRCh38
Lab
344
AMP-T2D consortium
27
Kyle Gaulton, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
4
Bing Ren, UCSD
1
Maike Sander, UCSD
1
Mark McCarthy, Oxford
Audit category:
70
inconsistent ontology term
1
audit script error
Audit category:
1
inconsistent assembly
files.file_type!
fastq
biosample_type!
primary cell
BIOSAMPLE
ASSAY
344 results
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total RNA-seq
ChIP-seq
ATAC-seq
DNase-seq
Hi-C
Capture-C
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
pCHi-C
snATAC-seq
tissue
islet of Langerhans
175
22
24
1
1
1
endocrine pancreas
16
body of pancreas
3
2
2
2
pancreas
1
2
1
1
1
cell line
EndoC_BH1
33
15
19
1
2
1
Panc1
13
1
1
in vitro differentiated cells
pancreatic PP cell
3
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