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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
315
total RNA-seq
148
ChIP-seq
80
ATAC-seq
11
snATAC-seq
10
MeRIP-seq
8
DNase-seq
6
single cell RNA-seq
4
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
pCHi-C
Assay category
323
Transcription
148
DNA binding
101
DNA accessibility
6
DNA methylation
4
3D chromatin structure
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
8
January, 2021
7
November, 2018
6
April, 2018
6
July, 2019
6
September, 2017
5
October, 2017
4
June, 2019
3
March, 2019
2
August, 2021
2
May, 2019
1
August, 2022
1
February, 2020
Available data
495
bam
431
bigWig
308
tsv
213
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
3
bedpe bed3+
3
hic
1
hdf5
Organism
588
Homo sapiens
Biosample type
501
tissue
primary cell
92
cell line
3
in vitro differentiated cells
Organ
746
liver
645
connective tissue
596
pancreas
489
adipose tissue
380
heart
316
kidney
265
brain
199
blood vessel
199
vasculature
158
bone element
139
artery
122
limb
118
epithelium
82
musculature of body
61
blood
61
bodily fluid
56
eye
43
nerve
37
embryo
25
spleen
20
lung
18
ureter
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
pericardium
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
562
AMP
34
T1D
Genome assembly (visualization)
471
hg19
442
GRCh38
Lab
531
AMP-T2D consortium
51
Kyle Gaulton, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
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
organ_slims!
pericardium
lab.title!
Bing Ren, UCSD
biosample_type!
primary cell
BIOSAMPLE
ASSAY
596 results
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total RNA-seq
ChIP-seq
ATAC-seq
snATAC-seq
MeRIP-seq
DNase-seq
single cell RNA-seq
Hi-C
WGBS
Capture-C
FAIRE-seq
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
pCHi-C
tissue
islet of Langerhans
277
50
57
7
4
1
6
1
1
1
body of pancreas
3
35
4
4
2
2
pancreas
2
16
4
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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