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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
178
ATAC-seq
143
single cell RNA-seq
135
ChIP-seq
72
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
428
Transcription
250
DNA accessibility
135
DNA binding
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
198
May, 2022
188
May, 2021
164
August, 2021
99
February, 2023
59
September, 2020
47
September, 2023
45
February, 2021
45
May, 2020
16
January, 2021
14
May, 2023
10
November, 2020
7
August, 2020
5
March, 2019
5
March, 2023
3
October, 2022
1
October, 2017
Available data
260
bigWig
230
bed narrowPeak
205
bam
195
fastq
153
zippedFastqFolder
112
tsv
84
tagAlign
64
xls
63
txt
7
hic
5
bedpe bed3+
3
cool
2
bed bed3+
2
bed broadPeak
1
bedpe
1
vcf
Organism
902
Homo sapiens
Biosample type
564
primary cell
293
tissue
in vitro differentiated cells
47
cell line
2
stem cell
Organ
221
pancreas
191
kidney
158
epithelium
71
liver
8
blood
8
bodily fluid
1
bone element
1
bone marrow
1
connective tissue
1
thymus
Project
324
HPAP
294
AMP
236
T1D
47
KPMP
4
community
1
ITG
Genome assembly (visualization)
276
hg19
269
GRCh38
Lab
AMP-T2D consortium
324
Klaus Kaestner, Upenn
296
Kyle Gaulton, UCSD
142
Katalin Susztak, Upenn
47
KPMP
40
Karen Mohlke, UNC
38
Bing Ren, UCSD
Xin Sun, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
4
Anna Gloyn, Oxford
2
Mark McCarthy, Oxford
1
ITG
1
Maike Sander, UCSD
1
Stephen Parker, UMich
Audit category:
30
audit script error
12
inconsistent ontology term
biosample_type!
in vitro differentiated cells
lab.title!
Xin Sun, UCSD
AMP-T2D consortium
BIOSAMPLE
ASSAY
906 results
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total RNA-seq
ATAC-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
29
31
1
pancreatic beta cell
11
16
16
1
exocrine cell
39
+ See 37 more…
tissue
kidney
49
75
58
6
1
islet of Langerhans
12
34
6
4
2
liver
20
20
pancreas
1
4
thymus
1
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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