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Sample GSM533583 Query DataSets for GSM533583
Status Public on Jul 07, 2010
Title 12R/11S - repeat 2 - mAdbID:65120
Sample type RNA
 
Channel 1
Source name Sensitive Isolate - Cy3
Organism Nakaseomyces glabratus
Characteristics developmental stage: log-phase culture
genotype/variation: WT
Extracted molecule total RNA
Extraction protocol Trizol Extraction Protocol
Other: Total RNA was isolated from log phase culture of C. glabrata grown in YPD using Trizole (Invitrogen) and RNeasy MiniElute cleanup kit (Qiagen).
Label cy3
Label protocol Cy3 Labeling Protocol
Other: Thirty micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy3-dUTP (GE Health Care).
 
Channel 2
Source name Resistant Isolate - Cy5
Organism Nakaseomyces glabratus
Characteristics developmental stage: log-phase culture
genotype/variation: CgPDR1 gain-of-function mutation
Extracted molecule total RNA
Extraction protocol Trizol Extraction Protocol
Other: Total RNA was isolated from log phase culture of C. glabrata grown in YPD using Trizole (Invitrogen) and RNeasy MiniElute cleanup kit (Qiagen).
Label cy5
Label protocol Cy5 Labeling Protocol
Other: Thirty micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy5-dUTP (GE Health Care).
 
 
Hybridization protocol Hybridization Protocol
Other: Microarray hybridization was done at the NIH/NIAID/RTB core facility. The 70-mer oligo arrays were prehybridized at 42°C in prehybridization buffer (5X SSC, 1% BSA, 0.1% SDS) for 30-60 min and then hybridized to the labelled cDNA in 50 ul of hybridization buffer (25% formamide, 5X SSC, 0.2% SDS, 20 ug/ml Poly (dA40-60), 200 ug/ml Cot-1 DNA, 80 ug/ml yeast t-RNA) overnight at 42°C. The microarrays were washed three times in wash buffer A (1X SSC, 0.05% SDS) and washing buffer B (0.1X SSC).
Scan protocol Creator: GenePix Pro 6.0.0.45
Scanner: GenePix 4000B [82425]
ScanPower: 100;; 100
LaserPower: 3.12;; 3.33
Temperature: 32.03
Description mAdb experiment ID: 65120
Data processing mAdb Data Processing
Calculation Method: Background correction was done using median intensity minus median background. Calculations were based on signals greater than 100 in both channels and excluding features designated as controls or flagged as bad or not found. Ratios were normalized using the 50th percentile (median).
 
Submission date Apr 15, 2010
Last update date Apr 30, 2013
Contact name Huei-Fung Tsai
E-mail(s) HT28T@NIH.GOV
Phone 301-496-8993
Fax 301-480-0512
Organization name NIH/NIAID
Department LCID
Lab CMS
Street address 10 Center Dr. Bldg. 10 Rm. 11N228
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL8174
Series (1)
GSE21352 Azole Resistance Mechanism in Candida glabrata Oropharyngeal Isolates

Data table header descriptions
ID_REF mAdb well id plus replicate number
VALUE GeneSpring normalized log2 ratio Cy5/Cy3

Data table
ID_REF VALUE
1658120_1 5.661
1652675_1 3.256
1654211_1 4.082
1657612_1 3.464
1658107_1 1.149
1654824_1 2.286
1653233_1 3.116
1653152_1 2.058
1652919_1 2.033
1653225_1 1.009
1657198_1 0.980
1653365_1 2.843
1656111_1
1657615_1
1656071_1 1.609
1657648_1 1.653
1654747_1 1.702
1652809_1 3.337
1653740_1 0.676
1657724_1 1.687

Total number of rows: 5887

Table truncated, full table size 89 Kbytes.




Supplementary file Size Download File type/resource
GSM533583.gpr.gz 601.1 Kb (ftp)(http) GPR
Processed data included within Sample table

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