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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
135
ChIP-seq
82
snATAC-seq
47
WGBS
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
135
DNA binding
82
DNA accessibility
47
DNA methylation
8
3D chromatin structure
1
DNA sequencing
Target of assay
117
histone
117
histone modification
65
broad histone mark
52
narrow histone mark
12
control
11
transcription factor
5
nucleotide modification
1
RNA binding protein
Date released
188
May, 2021
121
May, 2022
100
August, 2021
88
February, 2023
56
September, 2020
47
September, 2023
45
February, 2021
45
May, 2020
19
April, 2020
16
January, 2021
10
November, 2020
5
March, 2023
3
May, 2023
3
October, 2022
1
March, 2019
Available data
229
bigWig
186
bam
165
fastq
128
bed narrowPeak
114
zippedFastqFolder
112
tsv
84
tagAlign
63
txt
7
hic
5
bedpe bed3+
3
cool
2
bed bed3+
1
bedpe
1
vcf
Organism
742
Homo sapiens
Biosample type
515
primary cell
183
tissue
47
cell line
in vitro differentiated cells
2
stem cell
Organ
138
pancreas
116
kidney
109
epithelium
51
liver
19
lung
8
blood
8
bodily fluid
1
bone element
1
bone marrow
1
connective tissue
1
thymus
Project
275
HPAP
225
T1D
176
AMP
47
KPMP
19
LungMap
4
community
1
ITG
Genome assembly (visualization)
235
hg19
181
GRCh38
Lab
AMP-T2D consortium
275
Klaus Kaestner, Upenn
267
Kyle Gaulton, UCSD
67
Katalin Susztak, Upenn
47
KPMP
37
Bing Ren, UCSD
20
Karen Mohlke, UNC
19
Xin Sun, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
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
BIOSAMPLE
ASSAY
747 results
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total RNA-seq
single cell RNA-seq
ChIP-seq
snATAC-seq
WGBS
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
monocyte
53
84
1
Langerhans cell
85
48
pancreatic alpha cell
42
31
1
exocrine cell
39
CD8-positive, alpha-beta T cell
4
33
1
+ See 37 more…
tissue
kidney
49
58
6
1
islet of Langerhans
12
6
4
2
liver
20
lung
9
10
pancreas
1
4
+ See 1 more…
cell line
HepG2
9
18
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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