DASHR2_GEO_hg38 smRNA-seq peaks Track Settings

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DASHR v2.0 DASHR2_GEO_hg38 small RNA-seq called peaks

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Select subtracks by strand and tissue: (help)

All	*Strand*	Positive	Negative
*Tissue*
bone1 GSE85809
brainpfc3 GSE101521
brainpfc4 GSE64977
brainsfg1 GSE59286
breastmilk1 GSE75726
cd4plustcell2 GSE65515
cd8plustcellnaive1 GSE66650
eye1 GSE81254
foreskin-fibroblastcell1 GSE33584
gastric1 GSE89051
liver4 GSE57381
liver5 GSE87843
lung3 GSE83527
lung4 GSE63744
lung5 GSE37764
mature-erythrocyte1 GSE63703
monocyte-derived-macrophage1 GSE51307
oralmucosa1 GSE70666
ovary1 GSE64942
pancreatic-epithelial-cell1 GSE79147
peripheral-blood-B-cell1 GSE51359
peripheral-blood-mononucleated-cell1 GSE53080
plasma3 GSE53080
primary-BJ-fibroblast1 GSE62776
primary-fibroblast1 GSE53391
prostate1 GSE89193
prostate2 GSE80400
red-blood-cell1 GSE53080
serum3 GSE53439
serum4 GSE71578
serum5 GSE53080
umbilical-vein-endothelial-cell1 GSE53080
ventricular-myocardium1 GSE53080
wholeblood2 GSE67489
*Tissue*
All	*Strand*	Positive	Negative

List subtracks: only selected/visible all ()

	Tissue^↓1	Track Name^↓2
dense	brainpfc3 GSE101521	brainpfc3_GSE101521 [+] peaks	Data format
dense	brainpfc3 GSE101521	brainpfc3_GSE101521 [-] peaks	Data format
dense	foreskin-fibroblastcell1 GSE33584	foreskin-fibroblastcell1_GSE33584 [+] peaks	Data format
dense	foreskin-fibroblastcell1 GSE33584	foreskin-fibroblastcell1_GSE33584 [-] peaks	Data format
dense	lung5 GSE37764	lung5_GSE37764 [+] peaks	Data format
dense	lung5 GSE37764	lung5_GSE37764 [-] peaks	Data format
dense	monocyte-derived-macrophage1 GSE51307	monocyte-derived-macrophage1_GSE51307 [+] peaks	Data format
dense	monocyte-derived-macrophage1 GSE51307	monocyte-derived-macrophage1_GSE51307 [-] peaks	Data format
dense	peripheral-blood-B-cell1 GSE51359	peripheral-blood-B-cell1_GSE51359 [+] peaks	Data format
dense	peripheral-blood-B-cell1 GSE51359	peripheral-blood-B-cell1_GSE51359 [-] peaks	Data format
dense	peripheral-blood-mononucleated-cell1 GSE53080	peripheral-blood-mononucleated-cell1_GSE53080 [+] peaks	Data format
dense	plasma3 GSE53080	plasma3_GSE53080 [+] peaks	Data format
dense	red-blood-cell1 GSE53080	red-blood-cell1_GSE53080 [+] peaks	Data format
dense	serum5 GSE53080	serum5_GSE53080 [+] peaks	Data format
dense	umbilical-vein-endothelial-cell1 GSE53080	umbilical-vein-endothelial-cell1_GSE53080 [+] peaks	Data format
dense	ventricular-myocardium1 GSE53080	ventricular-myocardium1_GSE53080 [+] peaks	Data format
dense	peripheral-blood-mononucleated-cell1 GSE53080	peripheral-blood-mononucleated-cell1_GSE53080 [-] peaks	Data format
dense	plasma3 GSE53080	plasma3_GSE53080 [-] peaks	Data format
dense	red-blood-cell1 GSE53080	red-blood-cell1_GSE53080 [-] peaks	Data format
dense	serum5 GSE53080	serum5_GSE53080 [-] peaks	Data format
dense	umbilical-vein-endothelial-cell1 GSE53080	umbilical-vein-endothelial-cell1_GSE53080 [-] peaks	Data format
dense	ventricular-myocardium1 GSE53080	ventricular-myocardium1_GSE53080 [-] peaks	Data format
dense	primary-fibroblast1 GSE53391	primary-fibroblast1_GSE53391 [+] peaks	Data format
dense	primary-fibroblast1 GSE53391	primary-fibroblast1_GSE53391 [-] peaks	Data format
dense	serum3 GSE53439	serum3_GSE53439 [+] peaks	Data format
dense	serum3 GSE53439	serum3_GSE53439 [-] peaks	Data format
dense	liver4 GSE57381	liver4_GSE57381 [+] peaks	Data format
dense	liver4 GSE57381	liver4_GSE57381 [-] peaks	Data format
dense	brainsfg1 GSE59286	brainsfg1_GSE59286 [+] peaks	Data format
dense	brainsfg1 GSE59286	brainsfg1_GSE59286 [-] peaks	Data format
dense	primary-BJ-fibroblast1 GSE62776	primary-BJ-fibroblast1_GSE62776 [+] peaks	Data format
dense	primary-BJ-fibroblast1 GSE62776	primary-BJ-fibroblast1_GSE62776 [-] peaks	Data format
dense	mature-erythrocyte1 GSE63703	mature-erythrocyte1_GSE63703 [+] peaks	Data format
dense	mature-erythrocyte1 GSE63703	mature-erythrocyte1_GSE63703 [-] peaks	Data format
dense	lung4 GSE63744	lung4_GSE63744 [+] peaks	Data format
dense	lung4 GSE63744	lung4_GSE63744 [-] peaks	Data format
dense	ovary1 GSE64942	ovary1_GSE64942 [+] peaks	Data format
dense	ovary1 GSE64942	ovary1_GSE64942 [-] peaks	Data format
dense	brainpfc4 GSE64977	brainpfc4_GSE64977 [+] peaks	Data format
dense	brainpfc4 GSE64977	brainpfc4_GSE64977 [-] peaks	Data format
dense	cd4plustcell2 GSE65515	cd4plustcell2_GSE65515 [+] peaks	Data format
dense	cd4plustcell2 GSE65515	cd4plustcell2_GSE65515 [-] peaks	Data format
dense	cd8plustcellnaive1 GSE66650	cd8plustcellnaive1_GSE66650 [+] peaks	Data format
dense	cd8plustcellnaive1 GSE66650	cd8plustcellnaive1_GSE66650 [-] peaks	Data format
dense	wholeblood2 GSE67489	wholeblood2_GSE67489 [+] peaks	Data format
dense	wholeblood2 GSE67489	wholeblood2_GSE67489 [-] peaks	Data format
dense	oralmucosa1 GSE70666	oralmucosa1_GSE70666 [+] peaks	Data format
dense	oralmucosa1 GSE70666	oralmucosa1_GSE70666 [-] peaks	Data format
dense	serum4 GSE71578	serum4_GSE71578 [+] peaks	Data format
dense	serum4 GSE71578	serum4_GSE71578 [-] peaks	Data format
dense	breastmilk1 GSE75726	breastmilk1_GSE75726 [+] peaks	Data format
dense	breastmilk1 GSE75726	breastmilk1_GSE75726 [-] peaks	Data format
dense	pancreatic-epithelial-cell1 GSE79147	pancreatic-epithelial-cell1_GSE79147 [+] peaks	Data format
dense	pancreatic-epithelial-cell1 GSE79147	pancreatic-epithelial-cell1_GSE79147 [-] peaks	Data format
dense	prostate2 GSE80400	prostate2_GSE80400 [+] peaks	Data format
dense	prostate2 GSE80400	prostate2_GSE80400 [-] peaks	Data format
dense	eye1 GSE81254	eye1_GSE81254 [+] peaks	Data format
dense	eye1 GSE81254	eye1_GSE81254 [-] peaks	Data format
dense	lung3 GSE83527	lung3_GSE83527 [+] peaks	Data format
dense	lung3 GSE83527	lung3_GSE83527 [-] peaks	Data format
dense	bone1 GSE85809	bone1_GSE85809 [+] peaks	Data format
dense	bone1 GSE85809	bone1_GSE85809 [-] peaks	Data format
dense	liver5 GSE87843	liver5_GSE87843 [+] peaks	Data format
dense	liver5 GSE87843	liver5_GSE87843 [-] peaks	Data format
dense	gastric1 GSE89051	gastric1_GSE89051 [+] peaks	Data format
dense	gastric1 GSE89051	gastric1_GSE89051 [-] peaks	Data format
dense	prostate1 GSE89193	prostate1_GSE89193 [+] peaks	Data format
dense	prostate1 GSE89193	prostate1_GSE89193 [-] peaks	Data format

Assembly: Human Dec. 2013 (GRCh38/hg38)

DASHR v2.0 DASHR2 GEO hg38 small RNA signal tracks

This collection of tracks contains called small RNA peaks using SPAR small RNA-seq pipeline [3] across human tissues and cell types included in DASHR2 GEO data collection in DASHR v2.0 (see DASHR 2.0 data summary for information on data collections and included small RNA-seq experiments). Additional details are provided in (Kuksa PP et al, 2018) [1] and (Leung YY et al, 2016) [2].

Peak calling

Small RNA peaks were called using SPAR small RNA-seq pipeline (https://www.lisanwanglab.org/SPAR) described in reference [3].

DASHR 2.0. database

DASHR 2.0 database of small non-coding RNAs can be accessed at https://lisanwanglab.org/DASHRv2

References

Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung. DASHR v2.0: database of small human noncoding RNAs in human tissues and cell types. Bioinformatics, 2018 doi.org/10.1093/bioinformatics/bty709
Yuk Yee Leung*, Pavel P. Kuksa*, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, and Li-San Wang. DASHR: database of small human noncoding RNAs. Nucl. Acids Res., 2016 (Database Issue) doi:10.1093/nar/gkv1188
Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung. SPAR: small RNA-seq portal for analysis of sequencing experiments. NAR 2018 (Web Server issue). https://doi.org/10.1093/nar/gky330

Funding

National Institute of General Medical Sciences [R01-GM099962]; National Institute on Aging [U54-AG052427, U01-AG032984, U24-AG041689, UF1-AG047133], National Institute on Aging [T32-AG00255].