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Sample GSM2251776 Query DataSets for GSM2251776
Status Public on Oct 05, 2016
Title aft2 under 0 h iron starvation, replicate 3
Sample type RNA
 
Channel 1
Source name Yeasts in SD medium, iron-free
Organism Nakaseomyces glabratus
Characteristics strain: aft2
time: 0 h
replicate: 3
Treatment protocol For the time series, cultures were harvested by centrifugation and washed four times with iron-free SD, then incubated in iron-free SD.
Growth protocol Strains were cultured overnight in SD, harvested by centrifugation and washed four times in iron-free water. Cells were adjusted to 1×10E7 cells/ml in iron-free SD (pH 5.8) supplemented with 5 µM FeCl3 and pre-grown for 4 h at 37°C and 180 rpm.
Extracted molecule total RNA
Extraction protocol RNA was isolated with the RNAeasy Mini Kit (Qiagen) and quality was verified using the Agilent 2100 Bioanalyzer Nanochip system.
Label Cy5
Label protocol 1 µg high-quality RNA was used to generate cRNA fluorescently labeled with Cy5 CTP (GE Healthcare) using the One-Color Quick Amp labeling kit (Agilent).
 
Channel 2
Source name Yeast in YPD, log phase (common reference)
Organism Nakaseomyces glabratus
Characteristics strain: ATCC2001
time: 4 h
Treatment protocol For the time series, cultures were harvested by centrifugation and washed four times with iron-free SD, then incubated in iron-free SD.
Growth protocol Strains were cultured overnight in SD, harvested by centrifugation and washed four times in iron-free water. Cells were adjusted to 1×10E7 cells/ml in iron-free SD (pH 5.8) supplemented with 5 µM FeCl3 and pre-grown for 4 h at 37°C and 180 rpm.
Extracted molecule total RNA
Extraction protocol RNA was isolated with the RNAeasy Mini Kit (Qiagen) and quality was verified using the Agilent 2100 Bioanalyzer Nanochip system.
Label Cy3
Label protocol 1 µg high-quality RNA was used to generate cRNA fluorescently labeled with Cy5 CTP (GE Healthcare) using the One-Color Quick Amp labeling kit (Agilent).
 
 
Hybridization protocol Samples were hybridized using the Gene Expression Hybridization Kit (Agilent) according to manufacturer's instructions.
Scan protocol Scanned with a GenePix 4200AL (GenePix Pro 6.1, Auto PMT wavelengths 635/594, pixel size 5 µm)
Data processing Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.
 
Submission date Jul 25, 2016
Last update date Oct 05, 2016
Contact name Sascha Brunke
E-mail(s) sascha.brunke@hki-jena.de
Organization name Hans-Knöll-Institut
Department MPM
Street address Beutenbergstr. 11a
City Jena
ZIP/Postal code 07745
Country Germany
 
Platform ID GPL10713
Series (1)
GSE84816 Candida glabrata WT and mutants under iron starvation

Data table header descriptions
ID_REF
VALUE Lowess normalized log2 ratio sample/common reference (ch1/ch2)

Data table
ID_REF VALUE
CAGL0G07425g 0.66594505
CAGL0M03047g -0.018440247
CAGL0L11836g 0.1673317
CAGL0L08844g 0.46117115
CAGL0H05753g 0.30914116
CAGL0C04477g -0.4727583
CAGL0E00187g 0.018066406
CAGL0F00275g -0.073833466
CAGL0F04257g -0.75522804
CAGL0G00220g -0.49578094
CAGL0M06435g 0.26677215
CAGL0J02002g -0.32155037
CAGL0H07645g 2.1140368
CAGL0D02926g 0.015151978
CAGL0F00407g 1.4853945
CAGL0M12430g 1.0377274
CAGL0C03553g -0.25085258
CAGL0D05918g 0.6427946
CAGL0J10714g -0.5713434
CAGL0B00374g 0.9730153

Total number of rows: 5205

Table truncated, full table size 122 Kbytes.




Supplementary file Size Download File type/resource
GSM2251776_aft2_0_3.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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