DASHR1_GEO_hg38 smRNA-seq peaks Track Settings
 
DASHR v2.0 DASHR1_GEO_hg38 small RNA-seq called peaks

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 All Strand Positive  Negative 
Tissue
adipose1 GSE45159 
bcellgerminalcenter1 GSE22898 
bcellmemory1 GSE22898 
bcellnaive1 GSE22898 
bcellplasma1 GSE22898 
bladder1 GSE31616 
brainog1 SRA012516 
brainpfc1 GSE43335 
brainpfc2 GSE48552 
braintgm1 GSE46131 
breast1 GSE39162 
cd4plustcell1 GSE59944 
colon1 GSE46622 
colon2 GSE43550 
colonascendens1 GSE46622 
colonrectum1 GSE46622 
heart1 ERP000773 
heart2 SRA012516 
kidney1 ERP000773 
kidney2 GSE24457 
liver1 ERP000773 
liver2 SRA012516 
liver3 GSE21279 
lung1 GSE33858 
lung2 SRA012516 
monocytemacrophage1 GSE59944 
muscle1 SRA012516 
pancreas1 SRA012516 
pancreaticbetacell1 GSE47720 
pancreaticislet1 GSE47720 
peripheralbmc1 GSE19812 
peripheralbmc2 GSE37710 
plasma1 GSE52981 
serum1 GSE53439 
serum2 GSE34891 
skin1 GSE31037 
skin2 GSE53600 
spermatozoa1 GSE21191 
spleen1 GSE49624 
testiculargerm1 GSE31616 
wholeblood1 GSE46579 
wholeislet1 GSE52314 
Tissue
 All Strand Positive  Negative 
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dense
 brainpfc1 GSE43335  brainpfc1_GSE43335 [+] peaks   Schema 
dense
 brainpfc1 GSE43335  brainpfc1_GSE43335 [-] peaks   Schema 
    

DASHR v2.0 DASHR1 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 DASHR1 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].