|
| Status |
Public on Jul 01, 2016 |
| Title |
wild type 1h vs 0h experiment 1 WT 1h E1.b |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wild type 1h experiment 1
|
| Organism |
Candida albicans |
| Characteristics |
time: 1h
strain: CAI-10 (URA3/ura3Δ:: imm434) derived from CAF-3 (Fonzi & Irwin 1993)
|
| Treatment protocol |
At 0, 1, 3 and 5 hours from the shift to M199-pH 7.5 at 37°C cells ( 200 OD600) were collected, washed and frozen in liquid nitrogen
|
| Growth protocol |
Stationary phase from an overnight culture in YPD (1% Yeast Extract, 2% peptone, 2% glucose- 150 mM HEPES pH 6) at 30°C were pelletted and suspended in pre-warmed M199 (GIBCO + Earle's + L-glutamine)-150 mM HEPES buffered at pH 7.5, 2% glucose and incubated under agitation at 37°C at an initial optical density of 0.25
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was carried out using the QIAGEN Rneasy Midi Kit following manifacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
RNA samples were checked and processed at the Microarray Facility, Washingtn University at St.Louis, Mo, U.S.A. RNA was reversed transcribed into cDNA in the presence of CY3/Cy5 labeled NTPs
|
| |
|
| Channel 2 |
| Source name |
wild type 0h experiment 1
|
| Organism |
Candida albicans |
| Characteristics |
time: 0h
strain: CAI-10 (URA3/ura3Δ:: imm434) derived from CAF-3 (Fonzi & Irwin 1993)
|
| Treatment protocol |
At 0, 1, 3 and 5 hours from the shift to M199-pH 7.5 at 37°C cells ( 200 OD600) were collected, washed and frozen in liquid nitrogen
|
| Growth protocol |
Stationary phase from an overnight culture in YPD (1% Yeast Extract, 2% peptone, 2% glucose- 150 mM HEPES pH 6) at 30°C were pelletted and suspended in pre-warmed M199 (GIBCO + Earle's + L-glutamine)-150 mM HEPES buffered at pH 7.5, 2% glucose and incubated under agitation at 37°C at an initial optical density of 0.25
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was carried out using the QIAGEN Rneasy Midi Kit following manifacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
RNA samples were checked and processed at the Microarray Facility, Washingtn University at St.Louis, Mo, U.S.A. RNA was reversed transcribed into cDNA in the presence of CY3/Cy5 labeled NTPs
|
| |
|
| |
| Hybridization protocol |
A two step protocol was used (3DNA array 250 detection system, Genisphere, Hatfield, PA).
|
| Scan protocol |
Slides were scanned immediately after hybridization on a ScanArray express HY scanner (Perkin-Elmer)
|
| Data processing |
Processing of the raw data and normalization were carried out at the Microarray Facility, Washingtn University at St.Louis, Mo, U.S.A using the LOWESS normalization. The median of ratios were used for further analyses
Intra-array data processing was performed basically as previously described (Garcia et al., 2003), adapting the protocol to the microarray design used in our work. Flagged spots and spots with an average intensity minus background below the mean of the background for all the non-flagged spots in any of the channels (Cy3 or Cy5) were not retained for further analysis. Within this group, the spots showing in one channel a value of intensity minus background higher than 5 times the mean of the background for all spots in the microarray for that channel were recovered since they could correspond to potential on/off genes. Genes that did not have at least 2 valid replicates (the microarrays include 3 spots per ORF) or exceeded the intensity average by more than 1.5 S.D. were also discarded. Next, filtered data for each microarray were normalized using a Lowess normalization method.
|
| |
|
| Submission date |
Sep 20, 2013 |
| Last update date |
Jul 01, 2016 |
| Contact name |
Laura Popolo |
| E-mail(s) |
Laura.Popolo@unimi.it
|
| Phone |
+390250314919
|
| Organization name |
Università degli Studi di Milano
|
| Department |
Dipartimento di Bioscienze
|
| Street address |
Via Celoria 26
|
| City |
Milano |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL9545 |
| Series (1) |
| GSE51064 |
Transcriptional profiling of Candida albicans cells defective in glucan assembly and undergoing the Yeast to Hyphal transition |
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