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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
316
total RNA-seq
127
ChIP-seq
81
ATAC-seq
11
snATAC-seq
10
MeRIP-seq
6
single cell RNA-seq
5
Hi-C
4
WGBS
2
Capture-C
2
FAIRE-seq
2
RRBS
2
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
pCHi-C
Assay category
324
Transcription
127
DNA binding
95
DNA accessibility
6
DNA methylation
5
3D chromatin structure
Target of assay
81
histone
81
histone modification
45
broad histone mark
39
control
36
narrow histone mark
12
transcription factor
7
RNA binding protein
5
nucleotide modification
Date released
128
August, 2017
120
July, 2018
61
May, 2021
55
November, 2019
51
October, 2018
26
February, 2021
24
May, 2022
19
February, 2023
16
October, 2019
14
March, 2020
10
November, 2020
8
January, 2021
6
April, 2018
6
July, 2019
5
March, 2019
5
November, 2018
5
October, 2017
4
August, 2021
4
September, 2017
2
May, 2019
1
August, 2022
1
February, 2020
Available data
495
bam
431
bigWig
309
tsv
213
fastq
146
bed narrowPeak
69
bigBed narrowPeak
bed bed3+
21
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
563
Homo sapiens
Biosample type
478
tissue
primary cell
90
cell line
3
in vitro differentiated cells
Organ
770
liver
626
connective tissue
571
pancreas
483
adipose tissue
353
heart
250
kidney
238
brain
194
blood vessel
194
vasculature
158
bone element
135
artery
118
epithelium
86
limb
61
blood
61
bodily fluid
53
eye
49
musculature of body
nerve
34
embryo
24
spleen
20
lung
16
skeleton
5
gonad
5
ovary
2
intestine
2
pituitary gland
2
thymus
1
adrenal gland
1
esophagus
1
large intestine
1
lymph node
1
mammary gland
1
pericardium
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
537
AMP
34
T1D
Genome assembly (visualization)
446
hg19
414
GRCh38
Lab
502
AMP-T2D consortium
51
Kyle Gaulton, UCSD
10
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:
76
inconsistent ontology term
1
audit script error
Audit category:
5
inconsistent control read length
1
inconsistent assembly
organ_slims!
nerve
files.file_type!
bed bed3+
biosample_type!
primary cell
BIOSAMPLE
ASSAY
571 results
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total RNA-seq
ChIP-seq
ATAC-seq
snATAC-seq
MeRIP-seq
single cell RNA-seq
Hi-C
WGBS
Capture-C
FAIRE-seq
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
pCHi-C
tissue
islet of Langerhans
278
29
58
7
4
6
3
1
1
1
body of pancreas
3
35
4
2
2
pancreas
2
16
4
1
2
1
1
1
endocrine pancreas
16
cell line
EndoC_BH1
33
15
19
6
1
2
1
Panc1
13
in vitro differentiated cells
pancreatic PP cell
3
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