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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
1031
total RNA-seq
875
ChIP-seq
258
ATAC-seq
180
single cell RNA-seq
87
RNA microarray
29
pCHi-C
28
snATAC-seq
16
Hi-C
16
small RNA-seq
11
WGBS
4
FAIRE-seq
4
MeRIP-seq
3
snDrop-seq
2
DNase-seq
2
RRBS
1
CRISPR RNA-seq
1
CRISPRi RNA-seq
1
GRO-seq
Assay category
1229
Transcription
875
DNA binding
292
DNA accessibility
16
3D chromatin structure
13
DNA methylation
Target of assay
595
histone modification
594
histone
310
narrow histone mark
284
broad histone mark
188
control
94
transcription factor
28
RNA binding protein
3
other context
3
other post-translational modification
2
chromatin remodeller
2
nucleotide modification
Date released
545
February, 2021
253
August, 2017
238
October, 2019
229
August, 2021
193
May, 2020
120
July, 2018
115
May, 2019
95
February, 2023
80
April, 2019
76
November, 2017
74
October, 2018
66
May, 2022
63
July, 2019
51
December, 2017
47
September, 2023
44
March, 2020
40
May, 2021
40
May, 2024
40
November, 2019
25
February, 2020
19
April, 2020
19
October, 2017
15
May, 2023
11
November, 2018
8
January, 2021
7
December, 2018
7
January, 2019
6
April, 2018
6
September, 2017
4
March, 2019
4
November, 2020
3
December, 2019
3
January, 2018
2
March, 2023
1
August, 2022
Available data
1910
bam
1775
bigWig
1080
tsv
986
bed narrowPeak
561
bigBed narrowPeak
381
fastq
238
tagAlign
bed broadPeak
208
bed bed3+
176
bigBed broadPeak
157
txt
64
xls
25
bed bedMethyl
bigBed bedMethyl
11
hic
10
bedpe bed3+
6
csv
5
bed bed3
1
bedpe
1
tagAlign bed3+
Organism
2544
Homo sapiens
Biosample type
2539
tissue
primary cell
cell line
in vitro differentiated cells
10
stem cell
Organ
543
connective tissue
483
adipose tissue
479
pancreas
357
liver
279
heart
230
kidney
228
brain
158
bone element
127
blood vessel
127
vasculature
85
limb
69
artery
53
eye
41
nerve
34
musculature of body
22
spleen
20
lung
16
skeleton
15
epithelium
5
gonad
5
ovary
2
intestine
2
pituitary gland
2
thymus
1
adrenal gland
1
esophagus
1
large intestine
1
lymph node
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
2450
AMP
47
KPMP
31
T1D
19
LungMap
2
community
Genome assembly (visualization)
1655
GRCh38
1553
hg19
1
hg18
Lab
2197
AMP-T2D consortium
142
Katalin Susztak, Upenn
52
Kyle Gaulton, UCSD
47
KPMP
40
Karen Mohlke, UNC
40
Patrick T. Ellinor, Broad
19
Xin Sun, UCSD
4
Bing Ren, UCSD
4
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
1
Maike Sander, UCSD
1
Mark McCarthy, Oxford
Audit category:
91
inconsistent ontology term
27
inconsistent control
9
audit script error
Audit category:
24
missing controlled_by
Audit category:
8
inconsistent control read length
biosample_type!
cell line
in vitro differentiated cells
primary cell
files.file_type!
bed broadPeak
bigBed bedMethyl
BIOSAMPLE
ASSAY
2549 results
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total RNA-seq
ChIP-seq
ATAC-seq
single cell RNA-seq
RNA microarray
pCHi-C
snATAC-seq
Hi-C
small RNA-seq
WGBS
FAIRE-seq
MeRIP-seq
snDrop-seq
DNase-seq
RRBS
CRISPR RNA-seq
CRISPRi RNA-seq
GRO-seq
tissue
islet of Langerhans
292
65
66
6
4
7
3
1
4
1
adipose tissue
382
2
3
1
1
liver
167
145
20
1
1
1
1
3
kidney
49
27
75
64
6
1
1
bone element
84
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stem cell
hESC
3
1
SB Ad3.1
1
1
mesenchymal stem cell
1
mesendoderm
1
neural progenitor cell (neural stem cell)
1
+ See 1 more…
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