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Series GSE17789 Query DataSets for GSE17789
Status Public on Aug 25, 2009
Title Tiling microarray-based identification of small regulatory RNAs in the group A Streptococcus (GAS)
Organism Streptococcus pyogenes
Experiment type Expression profiling by genome tiling array
Non-coding RNA profiling by genome tiling array
Summary Small regulatory RNAs (sRNAs) represent a major mechanism of virulence regulation in several pathogens. To date, only three sRNAs have been described in GAS in any detail. To identify whether sRNAs are common within the GAS genome, we created a custom Affymetrix tiling microarray in which all intergenic regions (>49 bp) of the MGAS2221 genome were tiled at high density. Triplicate cultures of strain MGAS2221 in THY broth were grown to the exponential phase (O.D.600 of 0.5) of growth and RNA was isolated, converted to cDNA, fragmented, labeled, and hybridized to our custom array (one array per RNA sample [ hence three arrays total]). Our data identified the presence of 40 candidate sRNAs within the MGAS2221 genome.
 
Overall design Three cultures of MGAS2221 were grown in THY broth to the exponential (O.D. 0.5) phase of growth. Two volumes of RNA protect were added to the samples, the samples incubated at room temperature for 5 minutes, and the bacteria collected through centrifugation. Total RNA was isolated via a mechanical disruption method, converted to cDNA, fragmented, labeled, and hybridized to our Affymetrix microarray. Data was analyzed using tiling analysis software to combine the data from the three arrays and generate signal intensities.

The supplementary files 'GSE17789_2221sRNA_signal.bar' and 'GSE17789_2221sRNA_pvalue.bar' contain the signals and p-values, respectively, for Samples GSM444010-GSM444012. The BAR files are generated by TAS software using PM/MM signal intensities. Signal intensity data is reported in a linear scale; the p-value is reported in -10log10 scale. Probe analysis used a bandwidth of 40. Interval analysis used a threshold of 0, a maximum gap of 20, and a minimum run of 60.
 
Contributor(s) Sumby P
Citation(s) 19888332
Submission date Aug 24, 2009
Last update date Mar 21, 2012
Contact name Paul Sumby
Organization name University of Nevada
Department Microbiology & Immunology
Street address 1554 N. Virginia St.
City Reno
State/province NV
ZIP/Postal code 89557
Country USA
 
Platforms (1)
GPL6186 TMHRI_GAS
Samples (3)
GSM444010 2221sRNA1
GSM444011 2221sRNA2
GSM444012 2221sRNA3
This SubSeries is part of SuperSeries:
GSE17790 A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus
Relations
BioProject PRJNA123287

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
GSE17789_2221sRNA_pvalue.bar.gz 232.7 Kb (ftp)(http) BAR
GSE17789_2221sRNA_signal.bar.gz 235.6 Kb (ftp)(http) BAR
GSE17789_RAW.tar 33.8 Mb (http)(custom) TAR (of CEL)
Processed data are available on Series record
Processed data provided as supplementary file

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