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Series GSE46339 Query DataSets for GSE46339
Status Public on Aug 15, 2013
Title Genome-enabled studies of anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans
Organism Thiobacillus denitrificans ATCC 25259
Experiment type Expression profiling by array
Summary Investigation of whole genome gene expression level changes in anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans
 
Overall design Here we report on a study to identify genes associated with nitrate-dependent Fe(II) oxidation by whole-genome transcriptional (microarray) assays including the use of FeCO3, Fe2+, and U(IV) oxides as electron donors under denitrifying conditions. A 25 chip study using total RNA recovered from wild-type T. denitrificans was cultivated at 30oC under strictly anaerobic conditions with growth medium that contained 20 mM thiosulfate, 20 mM nitrate, and 30 mM bicarbonate (pH ~7) and exposed to 8 treatments. Each chip measures the expression level of 2832 ORFs with N 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
 
Contributor(s) Beller HR, Zhou P, Legler T, Chakicherla A, Kane SR, Letain T, O'Day P
Citation Beller, H. R., P. Zhou, T. C. Legler, A. Chakicherla, S. Kane, T. E. Letain, P.O'Day. Genome-enabled studies of anaerobic, nitrate-dependent iron oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans.Frontiers in Microbiology 4:249. doi: 10.3389/fmicb.2013.00249
Submission date Apr 24, 2013
Last update date Aug 15, 2013
Contact name Anu Chakicherla
E-mail(s) chakicherla1@llnl.gov
Organization name Lawrence Livermore National Lab
Street address 7000 East Avenue, Mail Stop: L-446
City Livermore
State/province CA
ZIP/Postal code 94551
Country USA
 
Platforms (1)
GPL3977 LLNL Thiobacillus denitrificans array (gene-view)
Samples (25)
GSM119288 ts.noH.O2.M2.X30829
GSM120793 ts.noH.NO3.M3.X30562
GSM120794 ts.noH.O2.M2.X30839
Relations
BioProject PRJNA198860

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE46339_All_773_956_calls.txt.gz 488.3 Kb (ftp)(http) TXT
GSE46339_All_773_956_pair.txt.gz 5.1 Mb (ftp)(http) TXT
GSE46339_All_norm_773_956_calls.txt.gz 890.4 Kb (ftp)(http) TXT
GSE46339_All_norm_773_956_pair.txt.gz 10.8 Mb (ftp)(http) TXT
GSE46339_RAW.tar 10.2 Mb (http)(custom) TAR
Processed data included within Sample table
Processed data are available on Series record

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