GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE81216 Query DataSets for GSE81216
Status Public on May 07, 2016
Title SpermBase - A database for sperm-borne RNA contents
Organisms Homo sapiens; Oryctolagus cuniculus; Mus musculus; Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Purpose: Sperm-borne RNA are particularly sensitive to degradation and methodology-induced bias, thus necessitating the use of a consistent, effective RNA extraction protocol for inter-species comparisons. To this end, we established SpermBase, an RNA expression database consisting of small and large RNA expression data obtained using consistent methodologies.
Methods: Total RNA was extracted from total sperm and sperm head samples using an RNA extraction protocol that required only slight, species-specific alterations at the lysis stage. Total RNA was subjected to either RNA-Seq (large RNA) or sncRNA-Seq (small RNA).
Results: By using a consistent methodology, we were able to perform a cross-species analysis on the conserved features of large and small sperm-borne RNAs. We identified conserved features in both populations of RNAs in the four mammalian species (i.e., mouse, rabbit, rat, and human) surveyed.
Conclusions: Our study demonstrates an effective, near-universal approach to the study of sperm-borne RNAs, and identifies conserved characteristics in the large and small RNA populations of mammalian sperm.
Overall design Total RNA was extracted from total sperm and sperm head samples and subjected to sncRNA-Seq or RNA-Seq.
Contributor(s) Schuster A, Tang C, Yu T, Yan W
Citation(s) 27628216
Submission date May 06, 2016
Last update date Jul 15, 2019
Contact name Wei Yan
Phone (775) 784-7765
Organization name University of Nevada
Department Physiology
Lab Wei Yan Lab
Street address 1664 N. Virginia Street
City reno
State/province NV
ZIP/Postal code 89557
Country USA
Platforms (6)
GPL16331 Ion Torrent PGM (Mus musculus)
GPL17301 Ion Torrent PGM (Homo sapiens)
GPL17303 Ion Torrent Proton (Homo sapiens)
Samples (32)
GSM2144775 mouse total sperm sncRNA-Seq rep1
GSM2144776 mouse total sperm sncRNA-Seq rep2
GSM2144777 mouse sperm head sncRNA-Seq rep1
BioProject PRJNA320896
SRA SRP074495

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE81216_spermbase.xlsx 1.9 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap