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Sample GSM275465 Query DataSets for GSM275465
Status Public on Oct 18, 2008
Title KT2440(pCAR1)_succinate_rep1_and_rep2
Sample type RNA
Source name Pseudomonas putida KT2440(pCAR1) grown on succinate at exponential phase
Organism Pseudomonas putida
Characteristics Strain KT2440(pCAR1), Carbon source: succinate, Growth phase: exponential
Treatment protocol A total of 1 × 10^9 cells were mixed with RNA Protect Bacteria reagent (Qiagen, Valencia, CA) as recommended by the manufacturer.
Growth protocol 100 ml of NMM-4 (Miyakoshi et al. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007 Oct;189(19):6849-60. PMID: 17675379) supplemented with 1.0 mg ml-1 sodium succinate or carbazole was inoculated by overnight culture in Luria broth to obtain initial optical densities at 600 nm (OD600) of 0.05. Cultures were incubated at 30˚C in a rotating shaker at 120 rpm to exponential phase.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min. After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel).
Label biotin
Label protocol Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12 µg of total RNA, 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~5 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.
Hybridization protocol Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 130 µl of the hybridization cocktail was hybridized at 45˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the FlexFS450-0002 protocol of GeneChip Fluidics station 450 (Affymetrix).
Scan protocol Signals were detected using GeneChip Scanner 3000 7G (Affymetrix).
Description KT2440(pCAR1)_succinate_rep1_and_rep2
Data processing The CEL files were generated using Affymetrix GCOS. The signal intensities at each probe were computed using Affymetrix TAS. The replications of CEL files were together converted into the BAR files using pCAR1_8b520435FF-3.bpmap for the forward strand and pCAR1_8b520435FR-3.bpmap for the reverse strand; the BAR files with header F indicate the forward strand and with header R indicate the reverse strand of pCAR1. The intensities were linearly scaled so that the median was 100. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.
Submission date Mar 17, 2008
Last update date Sep 09, 2008
Contact name Masatoshi Miyakoshi
Organization name Tohoku University
Department Department of Environmental Life Sciences
Lab Laboratory of Microbial Genetics
Street address Aoba-ku, Katahira, 2-1-1
City Sendai
State/province Miyagi
ZIP/Postal code 980-8577
Country Japan
Platform ID GPL6591
Series (1)
GSE10862 High-resolution mapping of the pCAR1 plasmid transcriptomes in Pseudomonas

Supplementary file Size Download File type/resource
GSM275465_061220_pCAR1_KT2440_SUC.CEL.gz 523.5 Kb (ftp)(http) CEL
GSM275465_070114_pCAR1_KT2440_SUC.CEL.gz 498.4 Kb (ftp)(http) CEL
GSM275465_F_KT2440(pCAR1) 138.4 Kb (ftp)(http) BAR
GSM275465_R_KT2440(pCAR1) 133.5 Kb (ftp)(http) BAR
Processed data provided as supplementary file

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