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Sample GSM2341997 Query DataSets for GSM2341997
Status Public on Oct 13, 2016
Title KT2440_dark
Sample type RNA
 
Source name cDNA prepared from dark culture of KT2440 in stationary phase
Organism Pseudomonas putida
Characteristics strain: KT2440
culture condition: dark
growth phase: stationary phase
Growth protocol P. putida KT2440 strain was grown in LB at 28°C at 135 strokes/min for 24 hrs under dark and light conditions.
Extracted molecule total RNA
Extraction protocol Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA). Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany) and RNeasy Midi kit (Qiagen). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI). After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel). cDNA was synthesized using SuperScript II (Invitrogen, Carlsbad, CA).
Label biotin
Label protocol Labelling of the cDNA or DNA was achieved using a GeneChip WT Double-Stranded DNATerminal Labeling Kit (Affymetrix, Santa Clara, CA).
 
Hybridization protocol The labelled samples were hybridized individually with each chip using a GeneChip Hybridization Oven 640 (Affymetrix) at 60 rpm and 50°C for 16 h. The chips were then washed and stained using a Hybridization, Wash and Stain Kit (Affymetrix) according to a modified version of the FleX450-0005 protocol of the GeneChip Fluidics station 450 (Affymetrix)
Scan protocol Signals were detected using a GeneChip Scanner 3000 7G (Affymetrix).
Description This is an Affymetrix custom-commercial tiling array that covers the Pseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density. BPMAP files are provided as supplementary files. KT2440b520511FR-3.bpmap represents the forward strand of KT2440 chromosome, and KT2440b520511FF-3.bpmap represents the reverse strand of KT2440 chromosome.
Data processing The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using KT2440b520511FR-3.bpmap for the forward strand and KT2440b520511FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.
 
Submission date Oct 12, 2016
Last update date Oct 13, 2016
Contact name Hideaki Nojiri
E-mail(s) anojiri@mail.ecc.u-tokyo.ac.jp
Phone +81-3-5841-3067
Organization name The University of Tokyo
Department Biotechnology Research Center
Lab Laboratory of Environmental Biochemistry
Street address 1-1-1 Yayoi, Bunkyo-ku
City Tokyo
ZIP/Postal code 113-8657
Country Japan
 
Platform ID GPL8296
Series (1)
GSE87863 The genome-wide transcriptional response to light in Pseudomonas putida KT2440

Supplementary file Size Download File type/resource
GSM2341997_F_KT2440_DA_signal.bar.gz 2.3 Mb (ftp)(http) BAR
GSM2341997_KT2440_dark_A.CEL.gz 9.9 Mb (ftp)(http) CEL
GSM2341997_R_KT2440_DA_signal.bar.gz 2.3 Mb (ftp)(http) BAR
Processed data provided as supplementary file

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