|
| Status |
Public on Nov 08, 2017 |
| Title |
S. Typhimurium_∆ompR pH 7.2+15% sucrose B |
| Sample type |
RNA |
| |
|
| Source name |
∆ompR pH 7.2+15% sucrose B
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S |
| Characteristics |
strain: 14028s
genotype: delta_ompR
ph: 7.2
sucrose status: 15% sucrose
|
| Growth protocol |
S. Typhimurium strains was grown in MgM media at pH 7.2 with(out) 15% (w/v) sucrose to O.D ~0.6.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated using an RNeasy mini kit (Qiagen).
|
| Label |
cyanine 3-CTP
|
| Label protocol |
100 ng of total RNA was labeled with Low Input Quick Amp WT Labeling Kit, One-Color (Agilent p/n 5190-2943) following manufacturer instruction (One-Color Microarray-Based Gene Expression, Analysis Low Input Quick Amp WT Labeling, version 2.0). Briefly, 100 ng of total RNA was converted into double-stranded cDNA by priming with an oligo-dT primer containing the recognition site for T7 RNA polymerase. In vitro transcription with T7 RNA polymerase was used to produce cyanine 3-CTP labeled cRNA.
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| |
|
| Hybridization protocol |
600ng of labeled cRNA was hybridized onto Agilent SurePrint G3 Custom 8x60K Microarray (G4102A) for 17 hours at 65oC, 10 rpm in Agilent hybridization oven. After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37oC
|
| Scan protocol |
Scanning was performed on Agilent High Resolution Microarray Scanner (C-model).
|
| Data processing |
Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1). The data analysis is done using a microarray specialized analysis software, Genespring GX.
Supplementary file includes: Raw Signal Values: The term “raw” signal values refer to the linear data after thresholding and summarization Summarization is performed by computing the geometric mean.Raw data filtered on Expression (20.0 - 731651.375)• Normalized Signal Values: ``Normalized'' value is the value generated after log transformation and normalization (Shift to 75 percentile) and baseline transformation.
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| |
|
| Submission date |
Nov 07, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
smarajit chakraborty |
| E-mail(s) |
chakrabortysmarajit@gmail.com
|
| Phone |
83682977
|
| Organization name |
Mechanobiology Institute
|
| Street address |
T-Lab, 5A Engineering Drive 1, NUS
|
| City |
singapore |
| ZIP/Postal code |
117411 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24239 |
| Series (2) |
| GSE106629 |
To compare the transcriptome of ompR null strains with wild-type strain of S. Typhimurium during osmotic stress |
| GSE106630 |
To compare the transcriptome of ompR null strains with wild-type strain of E. coli and S. Typhimurium during stress |
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