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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
219
total RNA-seq
71
ChIP-seq
57
ATAC-seq
11
snATAC-seq
10
MeRIP-seq
6
Hi-C
5
DNase-seq
5
single cell RNA-seq
2
Capture-C
2
RRBS
2
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
pCHi-C
Assay category
226
Transcription
73
DNA accessibility
71
DNA binding
6
3D chromatin structure
2
DNA methylation
Target of assay
51
histone
51
histone modification
26
broad histone mark
25
narrow histone mark
23
control
5
nucleotide modification
2
transcription factor
1
RNA binding protein
Date released
118
July, 2018
61
May, 2021
55
November, 2019
26
February, 2021
20
August, 2017
19
February, 2023
18
October, 2019
16
October, 2018
14
March, 2020
10
November, 2020
8
January, 2021
6
July, 2019
5
April, 2018
4
August, 2021
4
June, 2019
4
March, 2019
2
May, 2019
1
August, 2022
1
February, 2020
Available data
685
bam
608
bigWig
411
tsv
fastq
210
bed narrowPeak
91
bigBed narrowPeak
29
bed bed3+
20
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
391
Homo sapiens
Biosample type
292
tissue
92
cell line
5
primary cell
3
in vitro differentiated cells
Organ
583
connective tissue
447
adipose tissue
393
heart
392
pancreas
354
kidney
326
liver
259
brain
230
vasculature
227
blood vessel
184
epithelium
159
bone element
141
artery
122
limb
94
musculature of body
61
eye
43
nerve
22
vein
20
lung
18
ureter
16
skeleton
10
embryo
9
blood
9
bodily fluid
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
spleen
1
stomach
1
urinary bladder
Project
358
AMP
34
T1D
Genome assembly (visualization)
292
hg19
278
GRCh38
Lab
349
AMP-T2D consortium
Klaus Kaestner, Upenn
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:
76
inconsistent ontology term
1
audit script error
Audit category:
1
inconsistent assembly
files.file_type!
fastq
lab.title!
Klaus Kaestner, Upenn
month_released!
October, 2017
BIOSAMPLE
ASSAY
392 results
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total RNA-seq
ChIP-seq
ATAC-seq
snATAC-seq
MeRIP-seq
Hi-C
DNase-seq
single cell RNA-seq
Capture-C
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
pCHi-C
tissue
islet of Langerhans
181
22
38
7
4
3
1
endocrine pancreas
16
pancreas
2
4
1
2
1
1
body of pancreas
3
2
2
2
cell line
EndoC_BH1
33
15
19
6
1
2
1
Panc1
13
1
1
primary cell
pancreatic acinar cell
3
pancreatic ductal cell
1
pancreatic stellate cell
1
in vitro differentiated cells
pancreatic PP cell
3
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