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Sample GSM758881 Query DataSets for GSM758881
Status Public on Jul 13, 2011
Title hap43Δ mutant vs Wild type, in YEPD+BPS low iron medium, replicate 4
Sample type RNA
 
Channel 1
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)
 
Channel 2
Source name hap43Δ grown in YEPD+BPS (low iron)
Organism Candida albicans
Characteristics strain: SN694
genotype/variation: hap43Δ
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)
 
 
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 4 of 6. Low iron, Wt vs hap43DD
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 0.252
3657 0.031
11229 -0.1085
9819 0.7465
5038 -0.03
7237 -0.258
7535 -0.629
14182 -0.33
14862 0.0375
487 0.1045
2154 -0.2785
4213 0.54
2398 -0.052
1723 -0.4195
14056 -0.022
5055 -0.0085
7171 -0.1225
9489 0.317
10574 0.2045
11113 -0.6235

Total number of rows: 6099

Table truncated, full table size 72 Kbytes.




Supplementary file Size Download File type/resource
GSM758881_hap43KO-L_rep4.gpr.gz 1.5 Mb (ftp)(http) GPR
Processed data included within Sample table

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