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Sample GSM758864 Query DataSets for GSM758864
Status Public on Jul 13, 2011
Title Wild type YEPS vs BPS, replicate 3
Sample type RNA
 
Channel 1
Source name Wild type grown in YEPD (high iron)
Organism Candida albicans
Characteristics strain: SN250
genotype/variation: wild type
Growth protocol Saturated overnight cultures of sef1Δ (SN330), hap43Δ (SN694), sfu1Δ (SN515), and isogenic wild type C. albicans (SN250) were inoculated into YPD to OD600=10-4 and incubated with shaking at 30ºC. The next morning, logarithmically growing cells were diluted to OD600 0.01 in iron-replete (wild type and sfu1Δ) or low iron (wild type, sef1Δ, and hap43Δ) medium and incubated at 30°C for 5-6 hours before harvesting at OD600=0.5-0.6. 5-6 biological replicates were performed per strain per condition.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using a hot phenol method (Miller and Johnson, 2002).
Label Cy5
Label protocol 10 μg of each RNA was treated with DNase I (Turbo DNA-free kit, Ambion) and reverse transcribed using aminoallyl-dUTP and Superscript II (Invitrogen) according to manufacturers’ instructions. cDNA was labeled with Cy3 and Cy5 (Amersham)
 
Channel 2
Source name Wild type grown in YEPD+BPS (low iron)
Organism Candida albicans
Characteristics strain: SN250
genotype/variation: wild type
Growth protocol Saturated overnight cultures of sef1Δ (SN330), hap43Δ (SN694), sfu1Δ (SN515), and isogenic wild type C. albicans (SN250) were inoculated into YPD to OD600=10-4 and incubated with shaking at 30ºC. The next morning, logarithmically growing cells were diluted to OD600 0.01 in iron-replete (wild type and sfu1Δ) or low iron (wild type, sef1Δ, and hap43Δ) medium and incubated at 30°C for 5-6 hours before harvesting at OD600=0.5-0.6. 5-6 biological replicates were performed per strain per condition.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using a hot phenol method (Miller and Johnson, 2002).
Label Cy3
Label protocol 10 μg of each RNA was treated with DNase I (Turbo DNA-free kit, Ambion) and reverse transcribed using aminoallyl-dUTP and Superscript II (Invitrogen) according to manufacturers’ instructions. cDNA was labeled with Cy3 and Cy5 (Amersham)
 
 
Hybridization protocol Fluorescently labeled cDNAs from mutants were directly hybridized against those from wild type grown under the same conditions; dye flip controls were included. 6 additional arrays were performed using wild type grown under iron-replete vs. iron-limiting conditions. cDNA was labeled with Cy3 and Cy5 (Amersham), and 0.5 μg of each channel was hybridized to custom Agilent C. albicans ORF arrays (15,000 spots/array, 70-mer probes) following a protocol described by Hernday et al. (Methods Enzymol. 2010;470:737-58)
Scan protocol Arrays were scanned using a Genepix 4000A Axon scanner, and spots were filtered using GenePix Pro software.
Description Biological replicate 3 of 6. Wild type high iron vs. low iron
Data processing Data were normalized using Goulphar (LOWESS normalization) and subjected to One-class Significance Analysis of Microarrays (SAM) analysis with a median false discovery rate of 0.1%. Candidates meeting SAM criteria were also required to exhibit median 2-fold changes among 5-6 experiments.
 
Submission date Jul 12, 2011
Last update date Jul 13, 2011
Contact name Changbin Chen
E-mail(s) Changbin.Chen@ucsf.edu
Phone 4154768992
Fax 4154768201
Organization name University of California, San Francisco
Department Department of Microbiology & Immunology
Lab Dr. Suzanne Noble LAB
Street address HSE450, 513 Parnassus Avenue
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
 
Platform ID GPL13813
Series (2)
GSE30590 A unique iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis [Expression Array]
GSE30593 A unique iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis

Data table header descriptions
ID_REF
VALUE normalized log10 ratio representing test/reference

Data table
ID_REF VALUE
740 0.641
3657 -1.118
11229 -0.5185
9819 0.3815
5038 0.102
7237 0.297
7535 0.2715
14182 -2.54
14862 0.1485
487 -0.0225
2154 -0.34
4213 0.394
2398 0.1575
1723 -1.7935
14056 -0.4825
5055 0.657
7171 0.012
9489 1.3895
10574 0.364
11113 0.275

Total number of rows: 6099

Table truncated, full table size 72 Kbytes.




Supplementary file Size Download File type/resource
GSM758864_Wt_H_vs_L_rep3.gpr.gz 1.5 Mb (ftp)(http) GPR
Processed data included within Sample table

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