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Sample GSM2277993 Query DataSets for GSM2277993
Status Public on Jan 01, 2017
Title WtSt1
Sample type SRA
 
Source name Bacteria
Organism Pseudomonas putida
Characteristics strain/genotype: KT2440
growth phase: stationary
Treatment protocol For all experiments the overnight culture of P. putida was diluted to starting OD600 0.1 in 100 ml of LB. Cells were harvested at three time points on the growth curve: mid-exponential (OD600~0.5), transition (OD600~2.5), and stationary phase (twice doubling time after the transition phase). For size-selected library KB1 three biological replicates of wt and Δhfq strains were grown.
Growth protocol P. putida KT2440 was grown at 30 °C, 250 rpm and routinely cultured in LB medium according to standard protocols
Extracted molecule total RNA
Extraction protocol RNA extraction for cDNA library KB1 preparations was performed as previously described (Gómez-Lozano et al., 2012). Briefly, 10 ml of harvested culture was mixed with 0.2 volumes of STOP solution (95% [v/v] ethanol, 5% [v/v] phenol). Cells were centrifuged, 1 mL of Trizol (Invitrogen) was added and the samples were snap frozen. Total RNA was extracted and treated with DNase I (Fermentas). Total RNA integrity and quality were validated by Bioanalyzer (Agilent).
For KB1 cDNA library, RNA was size-selected (up to 500 nt) as described previously (Gómez-Lozano et al., 2012) using 10% polyacrylamide-urea gels containing urea (Bio-Rad) with some changes. Sample was depleted of rRNA using MICROBExpress Kit (Ambion) and treated with Tobacco Acid Pyrophosphatase TAP (Epicentre). Following the fragmentation with RNaseIII, libraries were prepared using TruSeq Small RNA Sample Preparation Kit (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description 7 C
Data processing The RNA-seq data was trimmed by Beckman
RNA-seq data was analysed with open source software Rockhopper (version 2.0.3) (McClure et al., 2013)
Differential gene and sRNA expression analysis were carried out with the webserver T-REx (de Jong et al., 2015) using the RPKM values generated in the Rockhopper analysis. Differential expression of genes was considered significant with a fold change ≥ 2 and adjusted p-value ≤ 0.05
Genome_build: GenBank accession no. NC_002947.3
Supplementary_files_format_and_content: One file with all the processed results in excel: Raw counts, Normalized counts, RPKM, Expression values, q-values
 
Submission date Aug 13, 2016
Last update date May 15, 2019
Contact name Klara Bojanovic
E-mail(s) klara.bojanovic@gmail.com
Phone 004524653766
Organization name Technical University of Denmark
Department Novo Nordisk Foundation Center for Biosustainability
Street address Building 220, Kemitorvet
City Kgs. Lyngby
ZIP/Postal code 2800
Country Denmark
 
Platform ID GPL19659
Series (1)
GSE85578 RNA-sequencing data from Pseudomonas putida KT2440 wild-type and Δhfq mutant
Relations
BioSample SAMN05572227
SRA SRX2020725

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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