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Sample GSM1465297 Query DataSets for GSM1465297
Status Public on Jul 18, 2017
Title t1_fluc_end_rep3
Sample type genomic
 
Channel 1
Source name candida albicans, t1, fluconazole, replicate3
Organism Candida albicans
Characteristics strain: T1
treatment: Fluconazole
Treatment protocol Resistance to antifungal drugs was monitored using the E-test assay method (AB biodisk, Biomerieux). Therefore, cells were grown to mid-log phase, washed in 1xPBS, and diluted to an OD600 of 0.015. 150μl of cells were plated on SD minus uracil agar plates (pH7) using glass beads and allowed to dry for 15-30 minutes before applying a fluconazole E-test strip (0.016– 256 μg/ml, AB Biodisk). Plates were incubated at 30°C and the MIC was determined after 48 hours. To test for clone diversity of highly resistant strains (MIC=256μg/ml; T1FH a-c) were plated on SD minus uracil agar plates and 3 single colonies were picked for DNA extraction (T1FH a-c).
Growth protocol Strains were grown in synthetic defined medium minus uracil (SD without uracil, 0.67% yeast nitrogen base, 2% glucose, 0,2% drop-out mix, with 2% agar for solid medium only) at 30°C.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using the Genomic-tip 100/G kit (Qiagen) according to manufacturer’s instructions. DNA was resuspended in EB-buffer and DNA quantity and integrity was assessed using the Quant-it™ Picogreen® ds DNA quantitation assay and by agarose gel electrophoresi.
Label Cy5
Label protocol Genomic DNA was digested with Alu I and RSA I, amplified, labelled and hybridized according to manufacturer’s instructions using the Agilent Genomic DNA enzymatic labelling Kit.
 
Channel 2
Source name candida albicans, t0, none, replicate3
Organism Candida albicans
Characteristics strain: T0
treatment: none
Treatment protocol Resistance to antifungal drugs was monitored using the E-test assay method (AB biodisk, Biomerieux). Therefore, cells were grown to mid-log phase, washed in 1xPBS, and diluted to an OD600 of 0.015. 150μl of cells were plated on SD minus uracil agar plates (pH7) using glass beads and allowed to dry for 15-30 minutes before applying a fluconazole E-test strip (0.016– 256 μg/ml, AB Biodisk). Plates were incubated at 30°C and the MIC was determined after 48 hours. To test for clone diversity of highly resistant strains (MIC=256μg/ml; T1FH a-c) were plated on SD minus uracil agar plates and 3 single colonies were picked for DNA extraction (T1FH a-c).
Growth protocol Strains were grown in synthetic defined medium minus uracil (SD without uracil, 0.67% yeast nitrogen base, 2% glucose, 0,2% drop-out mix, with 2% agar for solid medium only) at 30°C.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using the Genomic-tip 100/G kit (Qiagen) according to manufacturer’s instructions. DNA was resuspended in EB-buffer and DNA quantity and integrity was assessed using the Quant-it™ Picogreen® ds DNA quantitation assay and by agarose gel electrophoresi.
Label Cy3
Label protocol Genomic DNA was digested with Alu I and RSA I, amplified, labelled and hybridized according to manufacturer’s instructions using the Agilent Genomic DNA enzymatic labelling Kit.
 
 
Hybridization protocol Genomic DNA was digested with Alu I and RSA I, amplified, labelled and hybridized according to manufacturer’s instructions using the Agilent Genomic DNA enzymatic labelling Kit.
Scan protocol Arrays were scanned on an Agilent G2565AA microarray scanner and microarray scan data was extracted using Agilent feature extraction software.
Description T1FHc
Data processing Quality control was assessed with R/Bioconductor packages GLAD and arrayQualityMetrics. No significant bias was detected. The four samples presented statistically comparable distributions so no additional data processing was performed, taking the normalized LogRatio provided by Agilent feature extraction and processing software for the present values.
 
Submission date Aug 05, 2014
Last update date Jul 18, 2017
Contact name Tobias Weil
E-mail(s) tobias.weil@fmach.it
Organization name Fondazione Edmund Mach
Street address Via E. Mach, 1
City S. Michele all'Adige (TN)
ZIP/Postal code 38010
Country Italy
 
Platform ID GPL19026
Series (2)
GSE60120 Mistranslation accelerates the evolution of antifungal drug resistance in Candida albicans [CGH]
GSE60122 Mistranslation accelerates the evolution of antifungal drug resistance in Candida albicans

Data table header descriptions
ID_REF
VALUE Log10 Ratio Cy5/Cy3 representing T1/T0

Data table
ID_REF VALUE
4 -0.396
5 0.0171
6 -0.0526
8 -0.0115
9 -0.0532
11 0
12 0
13 0
16 0.0672
17 -0.0841
19 0.0445
20 0.013
21 0.0851
22 0.0636
23 -0.17
24 -0.0408
25 0.233
26 -0.0695
27 0.228
29 0.185

Total number of rows: 61979

Table truncated, full table size 749 Kbytes.




Supplementary file Size Download File type/resource
GSM1465297_1_3.txt.gz 4.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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