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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
164
total RNA-seq
109
ATAC-seq
94
ChIP-seq
17
pCHi-C
16
snATAC-seq
11
single cell RNA-seq
3
CRISPR genome editing followed by DNA sequencing
2
HiChIP
1
Hi-C
Assay category
175
Transcription
125
DNA accessibility
94
DNA binding
1
3D chromatin structure
Target of assay
134
histone
134
histone modification
74
broad histone mark
narrow histone mark
12
transcription factor
8
control
5
RNA binding protein
Date released
175
May, 2021
128
August, 2021
45
May, 2020
24
May, 2022
23
February, 2023
14
May, 2023
8
January, 2021
Available data
170
bigWig
164
bam
146
bed narrowPeak
96
tsv
64
xls
63
txt
44
tagAlign
24
fastq
2
bed bed3+
1
hic
Organism
417
Homo sapiens
Biosample type
194
tissue
181
primary cell
37
in vitro differentiated cells
5
cell line
Organ
142
kidney
51
pancreas
8
blood
bodily fluid
1
bone element
1
bone marrow
1
connective tissue
1
thymus
Project
229
AMP
188
T1D
Genome assembly (visualization)
215
GRCh38
189
hg19
Lab
3355
AMP-T2D consortium
324
Klaus Kaestner, Upenn
275
Kyle Gaulton, UCSD
142
Katalin Susztak, Upenn
47
KPMP
40
Karen Mohlke, UNC
36
Bing Ren, UCSD
25
Patrick T. Ellinor, Broad
19
Xin Sun, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
7
Struan F.A. Grant, CHOP
4
Anna Gloyn, Oxford
2
Mark McCarthy, Oxford
1
ITG
1
Maike Sander, UCSD
1
Stephen Parker, UMich
Audit category:
5
inconsistent ontology term
audit.NOT_COMPLIANT.category!
missing controlled_by
organ_slims!
bodily fluid
target.investigated_as!
narrow histone mark
BIOSAMPLE
ASSAY
417 results
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total RNA-seq
ATAC-seq
ChIP-seq
pCHi-C
snATAC-seq
single cell RNA-seq
CRISPR genome editing followed by DNA sequencing
HiChIP
Hi-C
tissue
kidney
49
75
6
11
1
islet of Langerhans
11
29
6
pancreas
1
4
thymus
1
primary cell
monocyte
53
44
1
CD8-positive, alpha-beta T cell
4
23
1
B cell
2
1
naive B cel
2
1
naive thymus-derived CD8-positive, alpha-beta T cell
2
1
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in vitro differentiated cells
embryonic stem cell
5
5
27
cell line
EndoC_BH1
3
2
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