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Sample GSM1413849 Query DataSets for GSM1413849
Status Public on Dec 15, 2014
Title JZ1691_Photosynthetic_Acetate_Rep1
Sample type RNA
 
Source name JZ1691 (ΔFnrL) cells grown photosynthetically on acetate
Organism Cereibacter sphaeroides
Characteristics strain: JZ1691 (ΔFnrL)
Growth protocol R. sphaeroides strains that were grown in 500 ml cultures in roux bottles photosynthetically (bubbling with 95% N2, 5% CO2) on Sistrom's minimal media (SIS) (or SIS media with succinate replaced with acetate) and harvested at exponential phase. Some cells were grown in the dark under anaerobic respiratory conditions (bubbling with 95% N2, 5% CO2) with pyruvate provided as the main carbon source and DMSO as electron acceptor.
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 JZ1691 (ΔFnrL) cells obtained under photosynthetic conditions using a growth medium containing acetate as the sole carbon source.
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 Dec 15, 2014
Contact name Timothy J Donohue
E-mail(s) tdonohue@bact.wisc.edu
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)
GSE58554 Global analysis of photosynthesis transcriptional regulatory networks [Expression profiling]
GSE58717 Global analysis of photosynthesis transcriptional regulatory networks

Data table header descriptions
ID_REF
VALUE Log2 RMA signal

Data table
ID_REF VALUE
855 6.64578799
856 10.2093818
857 5.969974723
858 7.422147341
859 8.001054275
860 7.57018757
861 10.67700038
862 7.970863405
863 8.546762576
864 7.989771918
865 8.719632124
866 8.709050816
867 7.747903946
868 7.569681521
869 8.330391654
870 9.355692269
871 8.351110597
872 7.327943957
873 8.663190917
874 7.387894863

Total number of rows: 4490

Table truncated, full table size 73 Kbytes.




Supplementary file Size Download File type/resource
GSM1413849_JZ1691_Acetate_1.CEL.gz 740.5 Kb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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