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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
148
ChIP-seq
81
ATAC-seq
10
MeRIP-seq
8
DNase-seq
6
Hi-C
single cell RNA-seq
4
WGBS
3
snATAC-seq
2
Capture-C
2
FAIRE-seq
2
RRBS
2
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
pCHi-C
Assay category
318
Transcription
148
DNA binding
94
DNA accessibility
6
3D chromatin structure
6
DNA methylation
Target of assay
93
histone
93
histone modification
51
broad histone mark
42
narrow histone mark
41
control
19
transcription factor
9
RNA binding protein
5
nucleotide modification
Date released
147
August, 2017
120
July, 2018
61
May, 2021
55
November, 2019
51
October, 2018
26
February, 2021
24
May, 2022
19
February, 2023
18
October, 2019
14
March, 2020
10
November, 2020
January, 2021
7
November, 2018
6
July, 2019
6
September, 2017
5
March, 2019
5
October, 2017
4
August, 2021
4
June, 2019
2
May, 2019
1
August, 2022
1
February, 2020
Available data
489
bam
425
bigWig
303
tsv
207
fastq
146
bed narrowPeak
69
bigBed narrowPeak
29
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
578
Homo sapiens
Biosample type
491
tissue
primary cell
92
cell line
3
in vitro differentiated cells
Organ
776
liver
645
connective tissue
586
pancreas
489
adipose tissue
287
heart
265
brain
kidney
193
blood vessel
193
vasculature
158
bone element
137
artery
122
limb
118
epithelium
81
musculature of body
61
blood
61
bodily fluid
56
eye
43
nerve
37
embryo
25
spleen
18
ureter
16
skeleton
11
lung
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
560
AMP
26
T1D
Genome assembly (visualization)
467
hg19
437
GRCh38
Lab
525
AMP-T2D consortium
43
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:
10
missing controlled_by
Audit category:
5
inconsistent control read length
2
inconsistent assembly
assay_title!
single cell RNA-seq
biosample_type!
primary cell
month_released!
January, 2021
organ_slims!
kidney
BIOSAMPLE
ASSAY
586 results
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total RNA-seq
ChIP-seq
ATAC-seq
MeRIP-seq
DNase-seq
Hi-C
WGBS
snATAC-seq
Capture-C
FAIRE-seq
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
pCHi-C
tissue
islet of Langerhans
278
50
58
4
1
3
3
1
1
body of pancreas
3
35
4
4
2
2
pancreas
2
16
2
1
2
1
1
1
endocrine pancreas
16
cell line
EndoC_BH1
33
15
19
6
1
2
1
Panc1
13
1
1
in vitro differentiated cells
pancreatic PP cell
3
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