Difference between revisions of "Streptococcus pneumoniae"

Revision as of 23:56, 3 November 2013

Microarray Papers

Reference Paper

Title: Genome of the Bacterium Streptococcus pneumoniae Strain R6

By Hoskins et al. (2001)

Web 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: Ogunniyi et al. 2012

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

Yadav et al. 2012

Web Link: [3]

PDF: PDF

Data at: [4]

Experiment Performed: Differential gene expression profile of Streptococcus pneumoniae early biofilm cells and planktonic cells

Replicates: 21 biological microarray replicates were used.

---Put in by Tauras: Please very experiment and 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

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

Pandya et al. 2009

Web Link: [5]

PDF: Not available (under copyright). May be downloaded directly from the link above.

Data at: [6]

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

4. Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors

Kazmierczak et al. 2003

Web Link: [7]

PDF: had trouble downloading it to computer, link is available at: [8]

Data at: [9]

Experiment Performed: Cell cultures were exposed to 4 different translation inhibitors to determine the effect on the transcript activity. The control used was a 1% DMSO culture that contained no antibiotics.

Replicates: 3 replicates done, along with Northern blot analysis.

Reference: Ng, WL, Kazmierczak, KM, Robertson, GT, Gilmour, R, & Winkler, ME (2003). Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors. Journal of bacteriology, 185(1): 359-370.

• Note: Ng is actually the authors last name. I thought it was a mistake too. Taur.vil (talk) 20:44, 31 October 2013 (PDT)

Found by Alina

5. Comparative Analysis of Growth-Phase-Dependent Gene Expression in Virulent and Avirulent Streptococcus pneumoniae Using a High-Density DNA Microarray

Ko et al. 2005

Web Link: growth dependent paper

PDF: Media:Growth_dependent_paper.pdf

Data at: Not posted by Kevin

Experiments Performed: Not posted by Kevin

Replicates: Not posted by Kevin

Reference: Ko, KS, Park, S, Oh, WS, Suh, JY, Oh, T, Ahn, S, et al. (2006). Comparative analysis of growth-phase-dependent gene expression in virulent and avirulent Streptococcus pneumoniae using a high-density DNA microarray. Molecules and cells, 21(1): 82-88.

Found by Kevin

6. Microarray analysis of Streptococcus pneumoniae gene expression changes to human lung epithelial cells

Song et al. 2008

Web Link: human lung paper

PDF: Media:Human_lung_paper.pdf

Data at: Not posted by Kevin

Experiments Performed: Not posted by Kevin

Replicates: Not posted by Kevin

Reference: Song, XM, Connor, W, Jalal, S, Hokamp, K, & Potter, AA (2008). Microarray analysis of Streptococcus pneumoniae gene expression changes to human lung epithelial cells. Canadian journal of microbiology, 54(3): 189-200.

Found by Kevin

Team

Team Leader: Alina

• Coder: Tauras
• Quality Assurance: Alina
• GenMAPP User: Kevin Meilak

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