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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
97
ChIP-seq
81
ATAC-seq
11
snATAC-seq
10
MeRIP-seq
8
DNase-seq
6
Hi-C
6
single cell RNA-seq
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
324
Transcription
102
DNA accessibility
97
DNA binding
6
3D chromatin structure
6
DNA methylation
Target of assay
63
histone
63
histone modification
32
broad histone mark
31
narrow histone mark
30
control
9
transcription factor
5
nucleotide modification
3
RNA binding protein
Date released
147
August, 2017
120
July, 2018
61
May, 2021
55
November, 2019
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
March, 2019
5
October, 2017
4
August, 2021
4
June, 2019
2
May, 2019
1
August, 2022
1
February, 2020
Available data
444
bam
391
bigWig
309
tsv
178
fastq
106
bed narrowPeak
29
bed bed3+
29
bigBed narrowPeak
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
541
Homo sapiens
Biosample type
454
tissue
primary cell
92
cell line
3
in vitro differentiated cells
Organ
777
liver
622
connective tissue
549
pancreas
466
adipose tissue
380
heart
265
brain
254
kidney
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
1
pericardium
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
515
AMP
34
T1D
Genome assembly (visualization)
433
hg19
403
GRCh38
Lab
480
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:
10
missing controlled_by
Audit category:
4
inconsistent control read length
2
inconsistent assembly
month_released!
October, 2018
files.file_type!
xls
biosample_type!
primary cell
BIOSAMPLE
ASSAY
549 results
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total RNA-seq
ChIP-seq
ATAC-seq
snATAC-seq
MeRIP-seq
DNase-seq
Hi-C
single cell RNA-seq
WGBS
Capture-C
FAIRE-seq
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
pCHi-C
tissue
islet of Langerhans
278
50
58
7
4
1
3
6
1
1
pancreas
2
14
4
2
1
2
1
1
1
body of pancreas
3
2
4
4
2
2
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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