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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
397
total RNA-seq
88
ATAC-seq
80
single cell RNA-seq
51
WGBS
30
ChIP-seq
11
snATAC-seq
9
Hi-C
5
MeRIP-seq
2
Capture-C
2
RRBS
2
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
pCHi-C
Assay category
479
Transcription
99
DNA accessibility
53
DNA methylation
30
DNA binding
9
3D chromatin structure
Target of assay
control
24
histone
24
histone modification
14
narrow histone mark
10
broad histone mark
6
transcription factor
5
nucleotide modification
1
RNA binding protein
Date released
157
July, 2018
118
August, 2017
86
May, 2022
57
May, 2021
56
February, 2023
39
April, 2018
32
February, 2021
26
September, 2018
22
November, 2019
19
September, 2020
11
March, 2020
8
January, 2021
7
August, 2020
6
July, 2019
5
March, 2019
5
November, 2020
5
October, 2019
4
August, 2021
4
November, 2018
3
August, 2018
3
October, 2022
2
October, 2018
1
August, 2022
1
February, 2020
1
June, 2018
1
October, 2017
Available data
665
bam
641
bigWig
441
fastq
417
tsv
bed narrowPeak
109
bigBed narrowPeak
80
zippedFastqFolder
45
bed bed3+
39
bed broadPeak
25
bigBed broadPeak
16
tagAlign
7
bedpe bed3+
7
hic
6
bed bedMethyl
6
bigBed bedMethyl
6
txt
3
cool
1
bedpe
1
hdf5
Organism
678
Homo sapiens
Biosample type
353
tissue
266
primary cell
60
cell line
Organ
679
pancreas
574
connective tissue
454
adipose tissue
343
epithelium
242
liver
182
heart
159
kidney
151
bone element
81
vasculature
80
blood vessel
58
artery
52
brain
30
musculature of body
27
eye
20
lung
16
embryo
13
limb
9
blood
9
bodily fluid
8
skeleton
7
vein
5
gonad
5
nerve
5
ovary
3
spleen
2
intestine
2
pericardium
2
thymus
1
adrenal gland
1
bone marrow
1
esophagus
1
large intestine
1
lymph node
mammary gland
1
pituitary gland
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
0
ureter
Project
497
AMP
152
HPAP
30
T1D
Genome assembly (visualization)
445
GRCh38
444
hg19
Lab
481
AMP-T2D consortium
152
Klaus Kaestner, Upenn
33
Kyle Gaulton, UCSD
5
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:
62
inconsistent ontology term
4
audit script error
Audit category:
21
missing controlled_by
Audit category:
1
inconsistent assembly
files.file_type!
bed narrowPeak
organ_slims!
mammary gland
target.investigated_as!
control
BIOSAMPLE
ASSAY
679 results
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total RNA-seq
ATAC-seq
single cell RNA-seq
WGBS
ChIP-seq
snATAC-seq
Hi-C
MeRIP-seq
Capture-C
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
pCHi-C
tissue
islet of Langerhans
278
21
6
17
7
3
2
1
pancreas
2
2
4
1
1
1
body of pancreas
3
2
2
primary cell
pancreatic alpha cell
52
29
12
31
1
pancreatic beta cell
21
16
12
16
1
pancreatic acinar cell
4
4
12
1
pancreatic ductal cell
4
10
pancreatic endocrine cell
12
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cell line
EndoC_BH1
33
18
1
3
2
1
Panc1
1
1
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