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Sample GSM1413836 Query DataSets for GSM1413836
Status Public on Jun 17, 2014
Title RSP_0489_Rep3
Sample type RNA
 
Source name ΔRSP_0489 deletion cells grown aerobically
Organism Cereibacter sphaeroides
Characteristics strain: ΔRSP_0489
Growth protocol R. sphaeroides strains that were grown in 500 ml cultures in roux bottles either photosynthetically (bubbling with 95% N2, 5% CO2) or aerobically (bubbling with 69% N2, 30% O2, 1% CO2) on Sistrom's minimal media and harvested at exponential phase.
Extracted molecule total RNA
Extraction protocol RNA was extracted from R. sphaeroides cells by hot acid phenol extraction.
Label biotin
Label protocol Synthesized cDNA was labeled with BioArray™ Terminal labeling kit with biotin-ddUTP
 
Hybridization protocol not provided
Scan protocol not provided
Description Gene expression data from a ΔRSP_0489 markerless deletion strain obtained under aerobic conditions.
Data processing Microarray datasets were normalized by Robust Multichip Average (RMA) to log2 scale with background adjustment and quantile normalization. Statistical analysis of normalized data to identify differentially expressed genes was done using the limma package. Correction for multiple testing was done using Benjamini-Hochberg correction. All analyses were conducted in the R statistical programming environment.
 
Submission date Jun 16, 2014
Last update date Jun 17, 2014
Contact name Timothy J Donohue
E-mail(s) [email protected]
Phone 608-265-8465
Organization name University of Wisconsin - Madison
Department Bacteriology
Lab Timothy Donohue
Street address 1552 University Avenue
City Madison
State/province WI
ZIP/Postal code 53726
Country USA
 
Platform ID GPL162
Series (2)
GSE58553 An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks [Affymetrix]
GSE58658 An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks

Data table header descriptions
ID_REF
VALUE Log2 RMA signal

Data table
ID_REF VALUE
855 6.596322733
856 11.50332334
857 6.084782062
858 7.565377749
859 9.549371346
860 7.760146502
861 11.79900886
862 7.853862443
863 8.818261105
864 8.221935828
865 8.572992151
866 8.961630073
867 7.593693484
868 7.676815056
869 9.144889092
870 9.565533471
871 8.782064142
872 7.385229107
873 9.578034933
874 7.358454147

Total number of rows: 4490

Table truncated, full table size 73 Kbytes.




Supplementary file Size Download File type/resource
GSM1413836_RSP_0489_3.CEL.gz 754.6 Kb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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