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Sample GSM1465305 Query DataSets for GSM1465305
Status Public on Jul 18, 2017
Title t0_control_end_rep1
Sample type RNA
 
Source name candida albicans, t0, end, replicate1
Organism Candida albicans
Characteristics strain: T0
treatment: not treated
time: end
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. Each passage the Fluconazole (Sigma Aldrich) concentration of the liquid (SD minus uracil) growth medium was adjusted to a concentration corresponding to twice the last measured MIC. Passages were pursued until strains were growing in liquid media containing a Fluconazole concentration of 256 μg/ml.
Growth protocol Candida albicans strains used in this study were engineered to exhibit different levels of Leucine misincorporation at Serine CUG codons. T0: control strain 3,2% Leu misincorporation (natural mistranslation); T1: 24,9% Leu misincorporation. These highly ambiguous strains were constructed on the basis of the strain SN148 (arg4 /arg4 leu2 /leu2 his1 /his1 ura3 ::imm43/ura3 ::imm43 iro1 ::imm43/iro1 ::imm43) using homologous recombination methodologies as described in Bezerra et al PNAS 2013.
Extracted molecule total RNA
Extraction protocol RNA was extracted from strains at the beginning (T0, T1), middle (T0FM, T1FM) and end (T0FH, T1FH) of the evolution experiment. Additionally,clones were evolved for an equal number of total passages without the drug to study effects caused by mistranslation and by the antifungal fluconazole (T0NF, T1NF). RNA was extracted from mid-exponential phase cells using the hot phenol method. DNase I (Invitrogen) treated RNA was resuspended in RNAse free water and RNA quantity and integrity was assessed using UV/Vis spectrometry (Nanodrop) and the 2100 Agilent Bioanalyzer respectively.
Label Cy3
Label protocol Same amounts of RNA extract (500 ng) from each replicate were amplified and Cy-3-labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies)
 
Hybridization protocol Custom gene expression SurePrint G3 microarrays (eArray accession number Candida_albicans_2007_1244213353206) were hybridized with CY3 labeled cRNA of growth duplicates according to manufacturer’s instructions (Agilent, Low Input Quick Amp Labelling kit).
Scan protocol Arrays were scanned on an Agilent G2505C microarray scanner and microarray scan data was extracted using Agilent feature extraction software.
Description t0NFa
Data processing Gene expression microarray raw data were normalized using limmaGUI software (R/ Bioconductor, Boston, MA, USA).
 
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 GPL19049
Series (2)
GSE60121 Mistranslation accelerates the evolution of antifungal drug resistance in Candida albicans [Gene expression]
GSE60122 Mistranslation accelerates the evolution of antifungal drug resistance in Candida albicans

Data table header descriptions
ID_REF
VALUE The matrix table contains the log2 expression level of the samples, after summarization and median normalization

Data table
ID_REF VALUE
1 10.0921653
10 2.8197272
100 10.8207790
1000 11.3071356
10000 7.8018296
10001 9.5715038
10003 13.1106019
10005 6.7923836
10009 7.2526063
10011 11.7072126
10012 13.8462309
10013 10.9303754
10014 11.2968075
10015 13.3692352
10017 8.1419900
10018 11.0976824
10019 9.7854422
1002 9.8204615
10026 10.5981087
10027 17.0234769

Total number of rows: 25821

Table truncated, full table size 412 Kbytes.




Supplementary file Size Download File type/resource
GSM1465305_t0UHa.txt.gz 1.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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