NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1236935 Query DataSets for GSM1236935
Status Public on Jul 01, 2016
Title mutant 1h vs 0h experiment 1 MUT 1h E1.a
Sample type RNA
 
Channel 1
Source name mutant 0h experiment 1
Organism Candida albicans
Characteristics time: 0h
strain: CAS-10 (phr1Δ:: hisG/phr1Δ ura3::imm434/URA3) derived from CAS-8, a Phr1- derivative of CAF3-1 (Saporito-Irwin et al., 1995)
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
 
Channel 2
Source name mutant 1h experiment 1
Organism Candida albicans
Characteristics time: 1h
strain: CAS-10 (phr1Δ:: hisG/phr1Δ ura3::imm434/URA3) derived from CAS-8, a Phr1- derivative of CAF3-1 (Saporito-Irwin et al., 1995)
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
 
 
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

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing treatment(time 1h, 3h or 5h)/control (time 0h)

Data table
ID_REF VALUE
1533
4893
8253
11613
14973
18333
1534 0.27
4894 0.48
8254
11614
14974
18334 0.39
693 2.51
4053 6.47
7413
10773 3.07
14133 1.20
17493
694 0.64
4054 1.48

Total number of rows: 6346

Table truncated, full table size 56 Kbytes.




Supplementary file Size Download File type/resource
GSM1236935_61.txt.gz 2.9 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap