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Series GSE104971 Query DataSets for GSE104971
Status Public on Mar 07, 2018
Title Staphylococcus aureus bona fide sRNAs in the model strain HG003
Organism Staphylococcus aureus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Accurate annotation of regulatory RNAs is a complex task but nevertheless essential as sRNA molecular and functional studies ensue from it. Several formerly considered small RNAs (sRNA) are now known to be parts of UTR transcripts. In light of experimental data, we review hundreds of Staphylococcus aureus putative regulatory RNAs. We pinpoint those that are likely acting in trans and are not expressed from the opposite strand of a coding gene. We conclude that HG003, a NCTC8325 derivative strain, has about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated.
 
Overall design Total RNA samples were extracted from HG003 grown in various biological conditions. All 16 RNA samples were pooled together for RNA sequencing. Pooled RNAs were processed using the MICROBExpress kit (Ambion, AM1905) as recommended by the suppliers, for rRNAs removal and before high-throughput sequencing using Illumina Genome Analyzer IIx generating single-end 40-nt reads.
 
Contributor(s) Rochat T, Bouloc P
Citation(s) 29515534
Submission date Oct 13, 2017
Last update date Jul 25, 2021
Contact name Tatiana Rochat
E-mail(s) tatiana.rochat@jouy.inra.fr
Organization name INRA
Lab Virologie et Immunologie Moléculaires
Street address Domaine de Vilvert
City Jouy-en-Josas
ZIP/Postal code 78350
Country France
 
Platforms (1)
GPL16057 Illumina Genome Analyzer IIx (Staphylococcus aureus)
Samples (1)
GSM2811258 Saureus_HG003_RNAseq
Relations
BioProject PRJNA414251
SRA SRP119942

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
GSE104971_RAW.tar 10.0 Kb (http)(custom) TAR (of GFF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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