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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
281
total RNA-seq
ATAC-seq
152
single cell RNA-seq
82
snATAC-seq
47
WGBS
23
ChIP-seq
17
pCHi-C
10
MeRIP-seq
8
Hi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
HiChIP
1
CRISPR RNA-seq
1
CRISPRi RNA-seq
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
437
Transcription
82
DNA accessibility
47
DNA methylation
23
DNA binding
8
3D chromatin structure
1
DNA sequencing
Target of assay
152
histone
histone modification
85
broad histone mark
67
narrow histone mark
16
transcription factor
12
control
6
RNA binding protein
5
nucleotide modification
Date released
121
May, 2022
97
August, 2021
88
February, 2023
74
May, 2021
56
September, 2020
47
September, 2023
45
February, 2021
45
May, 2020
19
April, 2020
16
January, 2021
10
November, 2020
5
March, 2023
5
May, 2024
3
May, 2023
3
October, 2022
1
March, 2019
Available data
165
fastq
117
bigWig
114
zippedFastqFolder
112
tsv
102
bam
63
txt
16
bed narrowPeak
7
hic
5
bedpe bed3+
3
cool
2
bed bed3+
1
bedpe
1
vcf
Organism
630
Homo sapiens
Biosample type
401
primary cell
188
tissue
44
cell line
in vitro differentiated cells
2
stem cell
Organ
138
pancreas
116
kidney
109
epithelium
48
liver
19
lung
8
blood
8
bodily fluid
5
heart
1
bone element
1
bone marrow
1
connective tissue
1
thymus
Project
275
HPAP
148
AMP
141
T1D
47
KPMP
19
LungMap
4
community
1
ITG
Genome assembly (visualization)
118
hg19
102
GRCh38
Lab
AMP-T2D consortium
275
Klaus Kaestner, Upenn
153
Kyle Gaulton, UCSD
67
Katalin Susztak, Upenn
47
KPMP
34
Bing Ren, UCSD
20
Karen Mohlke, UNC
19
Xin Sun, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
5
Patrick T. Ellinor, Broad
4
Anna Gloyn, Oxford
1
ITG
Audit category:
30
audit script error
12
inconsistent ontology term
lab.title!
AMP-T2D consortium
biosample_type!
in vitro differentiated cells
assay_title!
ATAC-seq
target.investigated_as!
histone modification
BIOSAMPLE
ASSAY
635 results
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total RNA-seq
single cell RNA-seq
snATAC-seq
WGBS
ChIP-seq
pCHi-C
MeRIP-seq
Hi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
HiChIP
CRISPR RNA-seq
CRISPRi RNA-seq
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
primary cell
Langerhans cell
85
48
pancreatic alpha cell
42
31
1
monocyte
53
1
exocrine cell
39
pancreatic beta cell
11
16
1
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tissue
kidney
49
58
6
1
islet of Langerhans
12
6
4
2
liver
20
lung
9
10
left cardiac atrium
5
+ See 2 more…
cell line
HepG2
9
15
1
2
1
EndoC_BH1
6
3
2
EndoC-BH1
1
1
HEK293T
2
Synthesized DNA
1
stem cell
SB Ad3.1
1
1
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