|
| Status |
Public on Oct 13, 2016 |
| Title |
KT2440_light |
| Sample type |
RNA |
| |
|
| Source name |
cDNA prepared from light culture of KT2440 in stationary phase
|
| Organism |
Pseudomonas putida |
| Characteristics |
strain: KT2440
culture condition: light
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 |
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