|
| Status |
Public on Jan 10, 2011 |
| Title |
wildtype_YNB pH 2.0_biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
wildtype cells, YNB pH 2.0 medium grown
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
genotype/variation: wildtype
|
| Treatment protocol |
Logarithmic phase wildtype and Cgyps1 delta were grown in YNB (pH 5.5) and YNB-pH 2.0 medium for 1 hr, cells were harvested, washed and stored in RNA later solution.
|
| Growth protocol |
Logarithmic phase wildtype and Cgyps1 cells were grown in YNB (pH 5.5) and YNB-pH 2.0 medium for 1 hr, cells were harvested, washed and stored in RNA later solution.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples stored in RNA later were sent to Genotypic Technology Ltd. Bangalore and RNA was isolated using Qiagen RNeasy Minikit (Cat No: 74106) as per the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.
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| |
|
| Hybridization protocol |
600ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)
|
| Scan protocol |
Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)
|
| Description |
Gene expression after 1hr growth in YNB (pH 2.0) medium
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1) and obtained background subtracted and spatially detrended Processed Signal intensities.
|
| |
|
| Submission date |
Sep 22, 2010 |
| Last update date |
Jan 10, 2011 |
| Contact name |
Rupinder Kaur |
| E-mail(s) |
rkaur@cdfd.org.in
|
| Organization name |
Centre for DNA Fingerprinting & Diagnostics
|
| Lab |
Lab of Fungal Pathogenesis
|
| Street address |
Building 7, Gruhakalpa, 5-4-399/B, Nampally
|
| City |
Hyderabad |
| ZIP/Postal code |
500001 |
| Country |
India |
| |
|
| Platform ID |
GPL10927 |
| Series (1) |
| GSE24267 |
Response of Candida glabrata to low pH |
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