DASHR2_GEO_hg38 smRNA-seq peaks Track Settings
 
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 
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dense
 wholeblood2 GSE67489  wholeblood2_GSE67489 [+] peaks   Schema 
dense
 wholeblood2 GSE67489  wholeblood2_GSE67489 [-] peaks   Schema 
    

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

  1. 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
  2. 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
  3. 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].