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Sample GSM1333721 Query DataSets for GSM1333721
Status Public on Dec 05, 2014
Title Y. pseudotuberculosis RNA-seq _persistent infection
Sample type SRA
 
Source name Persistent infection
Organism Yersinia pseudotuberculosis YPIII
Characteristics infection phase: Persistent infection data
polya depletion: poly(A) depleted RNA
rrna depleted: rRNA-depleted RNA
host: mouse
Treatment protocol Mouse were uninfected/infected for 2 days/ infected 42 days with Yersinia pseudotuberculosis YPIII with oral infection low dose (107CFUs)
Growth protocol Taken from mouse cecal tissue infected with Yersinia pseudotuberculosis YPIII at 42 days post infection
Extracted molecule total RNA
Extraction protocol Tissues are taken from the animal and kept in RNALater (Ambion) at +4C for overnight. Tissues are homogenized with two step homogenization for tissue and cell homogenization with a bead beater. RNA extracted based on Trizol method.
RNA libraries for sequencing were prepared using TruSeq RNA kits (Illumina, CA, USA) according to the manufacturer's instructions with the following changes. The RNA samples were EtOH precipitated and subsequent protocols (starting from cDNA synthesis in the Illumina provided protocol) automated using an MBS 1200 pipetting station (Nordiag AB, Sweden). All purification steps and gel-cuts were replaced by the magnetic bead clean-up methods described previously (Borgstrom et al., 2011)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description FVB/N cecal tissue at 42 days postinfection
Sample 2
Data processing Base trimming (5nt from 5' and 5nt from 3') with CLC Genomic Workbench 4.5.1
Trimmed reads from polyA and rRNA-depleted samples) were aligned to Yersinia pseudotuberculosis YPIII chromosome with 95% match, trimmed reads from polyA depeleted and non-rRNA depleted samples were aligned to NCBI 16SMicrobial Database with 100% match with CLC Genomic Workbench 4.5.1
Dublicate reads were removed with CLC Genomic Workbench 4.5.1
SNP calling was done with CLC Genomic Workbench
RPKMO values were calculated with statistical analysis on Gaussian data with Bonferroni correction as paired data with CLC Genomic Workbench
Genome_build: NC_010465 and NC_006153
Supplementary_files_format_and_content: Processed data files are in txt format. Processed data files contain expression values of ORFs of Yersinia pseudotuberculosis YPIII (NC_010465) and its virulence plasmid pYV (NC_006153) during early and late (sample 1 and 2) and for at 26C growth and 37 growth (Sample 6 and 7), processed data files contain number of reads mapped to 16SMicrobial NCBI database (Sample 3, 4 and 5)
 
Submission date Feb 24, 2014
Last update date May 15, 2019
Contact name Kemal Avican
E-mail(s) kemal.avican@umu.se
Organization name Umea University
Department Department of Molecular Biology
Lab Maria Fällman's Lab
Street address Building 6L
City Umea
ZIP/Postal code 90187
Country Sweden
 
Platform ID GPL18322
Series (2)
GSE55292 Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [RNA-seq]
GSE56477 Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection
Relations
BioSample SAMN02650477
SRA SRX475350

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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