ENCODE_GEO_hg38 smRNA-seq peaks Track Settings
 
DASHR v2.0 ENCODE_GEO_hg38 small RNA-seq called peaks

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Select subtracks by strand and tissue: (help)
 All Strand Positive  Negative 
Tissue
A549 SRR446329 
A549 SRR446330 
A549 SRR446331 
A549 SRR446332 
AG04450 SRR446309 
AG04450 SRR446310 
BJ SRR446315 
BJ SRR446316 
CD14plus SRR527681 
CD14plus SRR527682 
CD20plus SRR527679 
CD20plus SRR527680 
CD34plus SRR527586 
GM12878 SRR446392 
GM12878 SRR446393 
H1-hESC SRR446307 
H1-hESC SRR446308 
H1-neurons SRR527651 
H1-neurons SRR527652 
HAoAF SRR527663 
HAoAF SRR527664 
HAoEC SRR527673 
HAoEC SRR527674 
HCH SRR527667 
HCH SRR527668 
HeLa-S3 SRR446319 
HeLa-S3 SRR446320 
HepG2 SRR446333 
HepG2 SRR446334 
HFDPC SRR527669 
HFDPC SRR527670 
HMEpC SRR527693 
hMSC-AT SRR527675 
hMSC-AT SRR527676 
hMSC-BM SRR527649 
hMSC-BM SRR527650 
hMSC-UC SRR527689 
hMSC-UC SRR527690 
HOB SRR527665 
HOB SRR527666 
HPC-PL SRR527691 
HPC-PL SRR527692 
HPIEpC SRR527696 
HPIEpC SRR527697 
HSaVEC SRR527694 
HSaVEC SRR527695 
HVMF SRR527659 
HVMF SRR527660 
HWP SRR527685 
HWP SRR527686 
IMR90 SRR527621 
IMR90 SRR527622 
K562 SRR446398 
K562 SRR446399 
MCF-7 SRR446323 
MCF-7 SRR446324 
MCF-7 SRR446325 
MCF-7 SRR446326 
NHDF SRR527661 
NHDF SRR527662 
NHEK SRR446337 
NHEK SRR446338 
NHEM-f-M2 SRR527683 
NHEM-f-M2 SRR527684 
NHEM-M2 SRR527687 
NHEM-M2 SRR527688 
SkMC SRR527671 
SkMC SRR527672 
SK-N-SH-RA SRR446303 
SK-N-SH-RA SRR446304 
SK-N-SH SRR527595 
SK-N-SH SRR527596 
Tissue
 All Strand Positive  Negative 
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  Tissue↓1   Track Name↓2  
dense
 H1-neurons SRR527651  H1-neurons_SRR527651 [+] peaks   Schema 
dense
 H1-neurons SRR527651  H1-neurons_SRR527651 [-] peaks   Schema 
    

DASHR v2.0 ENCODE 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 ENCODE 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].