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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
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
285
Transcription
260
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
188
May, 2021
165
May, 2022
156
August, 2021
99
February, 2023
45
May, 2020
33
February, 2021
19
September, 2020
16
January, 2021
11
May, 2023
10
April, 2020
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
161
fastq
112
tsv
101
zippedFastqFolder
84
tagAlign
64
xls
55
txt
7
hic
5
bedpe bed3+
3
cool
2
bed bed3+
2
bed broadPeak
1
bedpe
1
vcf
Organism
768
Homo sapiens
Biosample type
479
primary cell
245
tissue
in vitro differentiated cells
47
cell line
2
stem cell
Organ
221
pancreas
158
epithelium
133
kidney
71
liver
10
lung
8
blood
8
bodily fluid
1
bone element
1
bone marrow
1
connective tissue
1
thymus
Project
283
AMP
239
HPAP
236
T1D
10
LungMap
4
community
1
ITG
Genome assembly (visualization)
276
hg19
269
GRCh38
Lab
AMP-T2D consortium
296
Kyle Gaulton, UCSD
239
Klaus Kaestner, Upenn
131
Katalin Susztak, Upenn
40
Karen Mohlke, UNC
38
Bing Ren, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
10
Xin Sun, UCSD
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
assay_title!
single cell RNA-seq
BIOSAMPLE
ASSAY
773 results
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total RNA-seq
ATAC-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
pancreatic alpha cell
42
29
31
1
Langerhans cell
48
pancreatic beta cell
11
16
16
1
exocrine cell
39
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tissue
kidney
49
75
6
1
islet of Langerhans
12
34
6
4
2
liver
20
20
lung
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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