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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
152
single cell RNA-seq
134
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
260
DNA accessibility
134
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
RNA binding protein
Date released
198
May, 2022
188
May, 2021
163
August, 2021
99
February, 2023
59
September, 2020
47
September, 2023
45
February, 2021
45
May, 2020
19
April, 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
259
bigWig
229
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
919
Homo sapiens
Biosample type
564
primary cell
312
tissue
in vitro differentiated cells
46
cell line
2
stem cell
Organ
221
pancreas
191
kidney
158
epithelium
70
liver
19
lung
8
blood
8
bodily fluid
1
bone element
1
bone marrow
1
connective tissue
1
thymus
Project
324
HPAP
293
AMP
236
T1D
47
KPMP
19
LungMap
4
community
1
ITG
Genome assembly (visualization)
275
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
37
Bing Ren, UCSD
19
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
lab.title!
AMP-T2D consortium
biosample_type!
in vitro differentiated cells
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
924 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
lung
9
10
pancreas
1
4
+ See 1 more…
cell line
HepG2
9
17
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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