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Sample GSM1111327 Query DataSets for GSM1111327
Status Public on Aug 15, 2013
Title WT iron x ∆fur iron- rep1
Sample type RNA
 
Channel 1
Source name WT- iron
Organism Caulobacter vibrioides NA1000
Characteristics genotype/variation: WT
growth protocol (iron conditions): NA1000 cells under iron sufficiency
Treatment protocol cultures were divided and treated with 100 µM FeSO4 (iron sufficiency) or 100 µM 2,2-dipyridyl (iron limitation)
Growth protocol overnight C. crescentus cultures were diluted to an optical density at 600 nm (OD600) of 0.1 in 35 ml of PYE medium and grown until midlog phase (OD600 ~ 0.5)
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy3
Label protocol Standard Cy3-dCTP and Cy5-dCTP incorporations
 
Channel 2
Source name ∆fur- iron
Organism Caulobacter vibrioides NA1000
Characteristics genotype/variation: fur mutant
growth protocol (iron conditions): NA1000 cells under iron sufficiency
Treatment protocol cultures were divided and treated with 100 µM FeSO4 (iron sufficiency) or 100 µM 2,2-dipyridyl (iron limitation)
Growth protocol overnight C. crescentus cultures were diluted to an optical density at 600 nm (OD600) of 0.1 in 35 ml of PYE medium and grown until midlog phase (OD600 ~ 0.5)
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy5
Label protocol Standard Cy3-dCTP and Cy5-dCTP incorporations
 
 
Hybridization protocol Standard Agilent protocol Agilent protocol Agilent protocol Agilent protocol
Scan protocol Standard Agilent protocol Agilent protocol
Data processing Data were extracted and normalized using Agilent Feature Extraction Software 9.0. Agilent output files were then opened using Excel and the log10 values extracted with no additional processing or filtering
 
Submission date Mar 31, 2013
Last update date Aug 16, 2013
Contact name Rogerio Lourenco
E-mail(s) lourenco@iq.usp.br
Organization name Universidade de Sao Paulo
Department Bioquimica
Street address Av. Prof. Lineu Prestes, 748
City Sao Paulo
State/province Sao Paulo
ZIP/Postal code 05508-900
Country Brazil
 
Platform ID GPL10469
Series (1)
GSE45653 Iron stimulon and Fur regulon

Data table header descriptions
ID_REF
VALUE lowess normalized log10 ratio (test/ reference)

Data table
ID_REF VALUE
1 0.000
2 0.000
3 0.000
4 0.000
5 0.000
6 0.000
7 0.000
8 0.000
9 0.000
10 0.000
11 0.000
12 1.446
13 0.030
14 0.090
15 0.000
16 0.000
17 0.000
18 -0.236
19 0.000
20 -0.221

Total number of rows: 45206

Table truncated, full table size 541 Kbytes.




Supplementary file Size Download File type/resource
GSM1111327_Fur_regulon-rep1.txt.gz 4.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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