Difference between revisions of "Streptococcus pneumoniae"

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:[[Media: R6_Reference_Genome_Paper.pdf|PDF]]
 
:[[Media: R6_Reference_Genome_Paper.pdf|PDF]]
  
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==Additional Microarray Papers==
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==Microarray Papers==
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# Author name and year
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===Reference Paper===
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#* PDF and link
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Title: Genome of the Bacterium Streptococcus pneumoniae Strain R6
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#* Full citation
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:By Hoskins et al. (2001)
 +
:[http://jb.asm.org/content/183/19/5709.full link]
 +
:[[Media: R6_Reference_Genome_Paper.pdf|PDF]]
  
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# Mukesh Kumar Yadav et al., 2012
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:Reference: Hoskins, J, Alborn, WE, Arnold, J, Blaszczak, LC, Burgett, S, DeHoff, BS, et al. (2001). Genome of the bacterium Streptococcus pneumoniae strain R6. Journal of Bacteriology, 183(19): 5709-5717.
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#* [[Media:Geneexpressionarticle1.pdf|PDF]][http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2012.00483.x/abstract|link]  Data: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15071]
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#* Yadav, M. K., Kwon, S. K., Cho, C. G., Park, S.-W., Chae, S.-W. and Song, J.-J. (2012), ''Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae. Microbiology and Immunology'', 56: 621–629.
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# Ng, WL, Kazmierczak, KM Robertson, GT, et al., 2003
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===1: Identification of Genes That Contribute to the Pathogenesis of Invasive Pneumococcal Disease by In Vivo Transcriptomic Analysis===
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Ogunniyi et al. 2012
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:Web Link: [http://iai.asm.org/cgi/content/full/80/9/3268]
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:PDF: [[Media:Article1.pdf|Article1.pdf]]
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:Data at: [http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=305&action=view&l=a]
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:Experiment Performed: This paper compared the gene expression between pneumococci in virulent and non-virulent strains that had grown in the nasopharynx, lungs, and blood of mice.
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:Replicates: There were 3 biological replicates in this data set.
 +
 
 +
 
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:Reference: Ogunniyi, AD, Mahdi, LK, Trappetti, C, Verhoeven, N, Mermans, D, Van der Hoek, MB, et al. (2012). Identification of genes that contribute to the pathogenesis of invasive pneumococcal disease by in vivo transcriptomic analysis. Infection and Immunity, 80(9): 3268-3278.
 +
:Found by [[User:Taur.vil|Tauras]]
 +
 
 +
===2: Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage===
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Pandya et al. 2009
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:Web Link: [http://www.sciencedirect.com/science/article/pii/S037811190900184X]
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:PDF: Not available (under copyright). May be downloaded directly from the link above.
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:Data at: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12607]
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:Experiment Performed: In this experiment, they compared transcription profiles as virulent ''Streptococcus pneumoniae'' crossed from the nasopharynx into the blood. The control was transcription in the nasopharynx, the experimental condition transcription in the blood.
 +
:Replicates: For this paper there are 2 biological replicates and 4 spot replicates
 +
 
 +
 
 +
:Reference: Pandya, U, Sinha, M, Luxon, BA, Watson, DA, & Niesel, DW (2009). Global transcription profiling and virulence potential of ''Streptococcus pneumoniae'' after serial passage. Gene, 443(1): 22-31.
 +
:Found by [[User:Taur.vil|Tauras]]
 +
 
 +
===2: Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae===
 +
Yadav et al. 2012
 +
:Web Link: [http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2012.00483.x/abstract]
 +
:PDF: [[Media:Geneexpressionarticle1.pdf|PDF]]
 +
:Data at: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15071]
 +
:Experiment Performed:
 +
:Replicates:
 +
 
 +
 
 +
:Reference: Yadav, MK, Kwon, SK, Cho, CG, Park, SW, Chae, SW, & Song, JJ (2012). Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae. Microbiology and Immunology, 56: 621–629.
 +
:Found by [[User:Ajvree|Alina]]
 +
 
 +
# Kazmierczak et al. 2003
 
#*Link to PDF (had trouble downloading it to computer): [http://jb.asm.org/content/185/1/359.full.pdf+html]  Data: [http://www.streppneumoniae.com/microarray_data.htm]
 
#*Link to PDF (had trouble downloading it to computer): [http://jb.asm.org/content/185/1/359.full.pdf+html]  Data: [http://www.streppneumoniae.com/microarray_data.htm]
 
#*Ng, WL, Kazmierczak, KM Robertson, GT, et al., 2003. ''Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors.'' Journal of Bacteriology. Volume 185, Issue 1, Pages 359-370.
 
#*Ng, WL, Kazmierczak, KM Robertson, GT, et al., 2003. ''Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors.'' Journal of Bacteriology. Volume 185, Issue 1, Pages 359-370.
 +
:Found by [[User:Ajvree|Alina]]
  
 
# Kwan Soo Ko et al., 2005
 
# Kwan Soo Ko et al., 2005
 
#*PDF [[Media:Growth_dependent_paper.pdf]]   
 
#*PDF [[Media:Growth_dependent_paper.pdf]]   
 
#*Kwan Soo Ko, Sulhee Park, Won Sup Oh, Ji-Yoeun Suh, TaeJeong Oh, Sungwhan Ahn, Jongsik Chun, Jae-Hoon Song, 2005. ''Comparative Analysis of Growth-Phase-Dependent Gene Expression in Virulent and Avirulent Streptococcus pneumoniae Using a High-Density DNA Microarray'', Mol. Cells, Vol. 21, No. 1, pp. 82-88.  
 
#*Kwan Soo Ko, Sulhee Park, Won Sup Oh, Ji-Yoeun Suh, TaeJeong Oh, Sungwhan Ahn, Jongsik Chun, Jae-Hoon Song, 2005. ''Comparative Analysis of Growth-Phase-Dependent Gene Expression in Virulent and Avirulent Streptococcus pneumoniae Using a High-Density DNA Microarray'', Mol. Cells, Vol. 21, No. 1, pp. 82-88.  
 +
:Found by [[User:Kmeilak|Kevin]]
  
 
# Xin-Ming Song et al., 2008
 
# Xin-Ming Song et al., 2008
 
#*PDF: [[Media:Human_lung_paper.pdf]]  
 
#*PDF: [[Media:Human_lung_paper.pdf]]  
 
#*Xin-Ming Song, Wayne Connor, Shakiba Jalal, Karsten Hokamp, Andrew A. Potter, 2008. ''Microarray analysis of Streptococcus pneumoniae gene expression changes to human lung epithelial cells''. Can. J. Microbiol. Vol. 54
 
#*Xin-Ming Song, Wayne Connor, Shakiba Jalal, Karsten Hokamp, Andrew A. Potter, 2008. ''Microarray analysis of Streptococcus pneumoniae gene expression changes to human lung epithelial cells''. Can. J. Microbiol. Vol. 54
 +
:Found by [[User:Kmeilak|Kevin]]
  
 
==Team==
 
==Team==

Revision as of 03:34, 1 November 2013

Contents

Reference Paper

link
PDF

Microarray Papers

Reference Paper

Title: Genome of the Bacterium Streptococcus pneumoniae Strain R6

By Hoskins et al. (2001)
link
PDF
Reference: Hoskins, J, Alborn, WE, Arnold, J, Blaszczak, LC, Burgett, S, DeHoff, BS, et al. (2001). Genome of the bacterium Streptococcus pneumoniae strain R6. Journal of Bacteriology, 183(19): 5709-5717.

1: Identification of Genes That Contribute to the Pathogenesis of Invasive Pneumococcal Disease by In Vivo Transcriptomic Analysis

Ogunniyi et al. 2012

Web Link: [1]
PDF: Article1.pdf
Data at: [2]
Experiment Performed: This paper compared the gene expression between pneumococci in virulent and non-virulent strains that had grown in the nasopharynx, lungs, and blood of mice.
Replicates: There were 3 biological replicates in this data set.


Reference: Ogunniyi, AD, Mahdi, LK, Trappetti, C, Verhoeven, N, Mermans, D, Van der Hoek, MB, et al. (2012). Identification of genes that contribute to the pathogenesis of invasive pneumococcal disease by in vivo transcriptomic analysis. Infection and Immunity, 80(9): 3268-3278.
Found by Tauras

2: Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage

Pandya et al. 2009

Web Link: [3]
PDF: Not available (under copyright). May be downloaded directly from the link above.
Data at: [4]
Experiment Performed: In this experiment, they compared transcription profiles as virulent Streptococcus pneumoniae crossed from the nasopharynx into the blood. The control was transcription in the nasopharynx, the experimental condition transcription in the blood.
Replicates: For this paper there are 2 biological replicates and 4 spot replicates


Reference: Pandya, U, Sinha, M, Luxon, BA, Watson, DA, & Niesel, DW (2009). Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage. Gene, 443(1): 22-31.
Found by Tauras

2: Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae

Yadav et al. 2012

Web Link: [5]
PDF: PDF
Data at: [6]
Experiment Performed:
Replicates:


Reference: Yadav, MK, Kwon, SK, Cho, CG, Park, SW, Chae, SW, & Song, JJ (2012). Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae. Microbiology and Immunology, 56: 621–629.
Found by Alina
  1. Kazmierczak et al. 2003
    • Link to PDF (had trouble downloading it to computer): [7] Data: [8]
    • Ng, WL, Kazmierczak, KM Robertson, GT, et al., 2003. Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors. Journal of Bacteriology. Volume 185, Issue 1, Pages 359-370.
Found by Alina
  1. Kwan Soo Ko et al., 2005
    • PDF Media:Growth_dependent_paper.pdf
    • Kwan Soo Ko, Sulhee Park, Won Sup Oh, Ji-Yoeun Suh, TaeJeong Oh, Sungwhan Ahn, Jongsik Chun, Jae-Hoon Song, 2005. Comparative Analysis of Growth-Phase-Dependent Gene Expression in Virulent and Avirulent Streptococcus pneumoniae Using a High-Density DNA Microarray, Mol. Cells, Vol. 21, No. 1, pp. 82-88.
Found by Kevin
  1. Xin-Ming Song et al., 2008
    • PDF: Media:Human_lung_paper.pdf
    • Xin-Ming Song, Wayne Connor, Shakiba Jalal, Karsten Hokamp, Andrew A. Potter, 2008. Microarray analysis of Streptococcus pneumoniae gene expression changes to human lung epithelial cells. Can. J. Microbiol. Vol. 54
Found by Kevin

Team

Team Leader: Alina


Main_Page

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