Streptococcus pneumoniae
From LMU BioDB 2013
Microarray Papers
Reference Paper
Title: Genome of the Bacterium Streptococcus pneumoniae Strain R6
- 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. A Transcription Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumoniae
Mahdi et. al. 2013
- Web Link: Transcription Factor paper
- PDF: Media:A_Transcription_Factor_Contributes_to_Pathogenesis_and_Virulence_in_Streptococcus_pneumoniae.pdf
- Data at: 1 and 2
- Experiments Performed: Effect of transcription factors on tissue-specific gene expression
- Replicates: 3 biological replicates, 1 technical for link 1; 3 biological replicates, 0 technical for link 2
- Reference: : Mahdi LK, Ebrahimie E, Adelson DL, Paton JC, Ogunniyi AD (2013) A Transcription Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumoniae. PLoS ONE 8(8): e70862. doi:10.1371/journal.pone.0070862
- Found by Kevin
6. Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production
Sanchez et. al. 2011
- Web Link: Biofilm paper
- PDF: Media:Biofilms_paper.pdf
- Data at: GEO link
- Experiments Performed: Examined genes related to biofilm formation of Streptococcus pneumoniae
- Replicates: 3 biological replicates, 3+ technical replicates
- Reference: Sanchez CJ, Kumar N, Lizcano A, Shivshankar P, Dunning Hotopp JC, et al. (2011) Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production. PLoS ONE 6(12): e28738. doi:10.1371/journal.pone.0028738
- Found by Kevin
Team
Team Leader: Alina
- Coder: Tauras
- Quality Assurance: Alina
- GenMAPP User: Kevin Meilak
