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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
175
ChIP-seq
152
single cell RNA-seq
snATAC-seq
47
WGBS
17
pCHi-C
10
MeRIP-seq
8
Hi-C
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
178
DNA accessibility
175
DNA binding
47
DNA methylation
8
3D chromatin structure
1
DNA sequencing
Target of assay
152
histone
152
histone modification
85
broad histone mark
67
narrow histone mark
16
transcription factor
12
control
6
RNA binding protein
5
nucleotide modification
Date released
188
May, 2021
177
May, 2022
153
August, 2021
97
February, 2023
59
September, 2020
47
September, 2023
45
May, 2020
40
May, 2024
18
February, 2021
14
May, 2023
10
November, 2020
9
April, 2020
7
August, 2020
5
March, 2019
5
March, 2023
3
October, 2022
1
October, 2017
Available data
300
bigWig
270
bed narrowPeak
205
bam
168
fastq
132
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
874
Homo sapiens
Biosample type
508
primary cell
326
tissue
in vitro differentiated cells
42
cell line
2
stem cell
Organ
211
pancreas
183
kidney
158
epithelium
69
liver
40
heart
9
lung
1
bone element
1
bone marrow
1
connective tissue
1
thymus
Project
323
AMP
276
HPAP
218
T1D
47
KPMP
9
LungMap
4
community
1
ITG
Genome assembly (visualization)
309
GRCh38
276
hg19
Lab
AMP-T2D consortium
278
Kyle Gaulton, UCSD
276
Klaus Kaestner, Upenn
136
Katalin Susztak, Upenn
47
KPMP
40
Karen Mohlke, UNC
40
Patrick T. Ellinor, Broad
33
Bing Ren, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
9
Xin Sun, UCSD
4
Anna Gloyn, Oxford
2
Mark McCarthy, Oxford
1
ITG
1
Maike Sander, UCSD
1
Stephen Parker, UMich
Audit category:
11
inconsistent ontology term
3
audit script error
assay_title!
STARR-seq
snATAC-seq
biosample_type!
in vitro differentiated cells
lab.title!
AMP-T2D consortium
BIOSAMPLE
ASSAY
878 results
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total RNA-seq
ATAC-seq
ChIP-seq
single cell RNA-seq
WGBS
pCHi-C
MeRIP-seq
Hi-C
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
85
pancreatic beta cell
11
16
16
1
exocrine cell
39
+ See 36 more…
tissue
kidney
49
75
58
1
islet of Langerhans
12
34
4
2
left cardiac atrium
40
liver
20
20
lung
9
+ See 2 more…
cell line
HepG2
9
18
1
1
EndoC_BH1
6
3
2
EndoC-BH1
1
1
stem cell
SB Ad3.1
1
1
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