g3 phylochipe 16s rrna microarray-based assay  (Second Genome Inc)

Journal: Current Issues in Molecular Biology

Article Title: The Effects of Ionizing Radiation on Gut Microbiota: What Can Animal Models Tell Us?—A Systematic Review

doi: 10.3390/cimb45050249

Figure Lengend Snippet: Literature search algorithm—PubMed; EMBASE (via OVID); and Cochrane Library.

Article Snippet: , Lam V, 2012 [ ] / Interventional , Rats WAG/RijCmcr (Wistar) Male 5 weeks / N = 10 (n = 5/group) , qPCR and 16S rRNA / Second Genome Inc. G3 PhyloChipe 16S rRNA microarray-based assay / Fecal N = 4 D0 and days 4, 11, and 21 post-irradiation , Composition Proteobacteria increased almost 1000-fold 4 days after 10 Gy and then returned to control values. 18 Gy prolonged increase over 5 days compared to over 3 days observed after 10 Gy Bacteroidetes—less affected Cyanobacteria OTU 31,902 increased Clostridia —less affected Clostridia OTU 39,153 decreased OTU 42,924 unchanged Bacteroidales —increased Lactobacillaceae and Streptococcaceae —increased Peptostreptococcaceae —unchanged Clostridiaceae —unchanged abundance but 47 separate OTUs decreased.

Techniques:

Journal: Current Issues in Molecular Biology

Article Title: The Effects of Ionizing Radiation on Gut Microbiota: What Can Animal Models Tell Us?—A Systematic Review

doi: 10.3390/cimb45050249

Figure Lengend Snippet: Summary of study characteristics, demographics, radiation type, sample collection and analysis, and main findings of the eligible studies with mice.

Article Snippet: , Lam V, 2012 [ ] / Interventional , Rats WAG/RijCmcr (Wistar) Male 5 weeks / N = 10 (n = 5/group) , qPCR and 16S rRNA / Second Genome Inc. G3 PhyloChipe 16S rRNA microarray-based assay / Fecal N = 4 D0 and days 4, 11, and 21 post-irradiation , Composition Proteobacteria increased almost 1000-fold 4 days after 10 Gy and then returned to control values. 18 Gy prolonged increase over 5 days compared to over 3 days observed after 10 Gy Bacteroidetes—less affected Cyanobacteria OTU 31,902 increased Clostridia —less affected Clostridia OTU 39,153 decreased OTU 42,924 unchanged Bacteroidales —increased Lactobacillaceae and Streptococcaceae —increased Peptostreptococcaceae —unchanged Clostridiaceae —unchanged abundance but 47 separate OTUs decreased.

Techniques: Irradiation, Control, Bacteria, DNA Extraction

Journal: Current Issues in Molecular Biology

Article Title: The Effects of Ionizing Radiation on Gut Microbiota: What Can Animal Models Tell Us?—A Systematic Review

doi: 10.3390/cimb45050249

Figure Lengend Snippet: Summary of study characteristics, demographics, radiation type, sample collection and analysis, and main findings of the eligible studies in animals (except mice).

Article Snippet: , Lam V, 2012 [ ] / Interventional , Rats WAG/RijCmcr (Wistar) Male 5 weeks / N = 10 (n = 5/group) , qPCR and 16S rRNA / Second Genome Inc. G3 PhyloChipe 16S rRNA microarray-based assay / Fecal N = 4 D0 and days 4, 11, and 21 post-irradiation , Composition Proteobacteria increased almost 1000-fold 4 days after 10 Gy and then returned to control values. 18 Gy prolonged increase over 5 days compared to over 3 days observed after 10 Gy Bacteroidetes—less affected Cyanobacteria OTU 31,902 increased Clostridia —less affected Clostridia OTU 39,153 decreased OTU 42,924 unchanged Bacteroidales —increased Lactobacillaceae and Streptococcaceae —increased Peptostreptococcaceae —unchanged Clostridiaceae —unchanged abundance but 47 separate OTUs decreased.

Techniques: Irradiation, Real-time Polymerase Chain Reaction, Microarray, Control, Bacteria, Activity Assay

Journal: PLoS ONE

Article Title: Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill

doi: 10.1371/journal.pone.0041305

Figure Lengend Snippet: Number of bacterial OTUs detected by PhyloChip in Inlet and Marsh sediments for June, July, and September 2010.

Article Snippet: Bacterial 16S rRNA gene diversity was assessed for June, July, and September 2010 sediments using the G3 PhyloChip, an Affymetrix platform microarray.

Techniques:

Journal: PLoS ONE

Article Title: Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill

doi: 10.1371/journal.pone.0041305

Figure Lengend Snippet: Resemblance matrix generated using Bray Curtis similarity and based on the relative abundance of taxa identified by PhyloChip analysis.

Article Snippet: Bacterial 16S rRNA gene diversity was assessed for June, July, and September 2010 sediments using the G3 PhyloChip, an Affymetrix platform microarray.

Techniques: Generated

Journal: PLoS ONE

Article Title: Coupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species

doi: 10.1371/journal.pone.0099801

Figure Lengend Snippet: A: Ordination analysis of PhyloChip G3 data based on weighted UniFrac measure of eOTU abundances followed by non-metric multidimensional scaling (NMDS). Stress for NMDS of archaeal eOTUs (#37): 0.0088. Stress for NMDS of bacterial eOTUs (#1300): 0.0223. B: Heatmap displaying significantly different families found between the two biofilm types, MSI-BF and SM-BF by PhyloChip G3 assay. Significance is based on aggregated HybScores of eOTUs on family level followed by a Welch-test. For false discovery detection please see . C: Ordination analysis of SR-FTIR data based on a linear discriminant analysis and principal component analysis (PCA-LDA) in the spectral region of 2800–3100 cm −1 on the archaea spectra extracted from the maps from the three different locations. On the right there is the plot of PCA-LDA loadings. PCA-LDA1 explains for the 93.4% of the variance, PCA-LDA2 for 5.3% and PCA-LDA3 for 0.9%. Arrows point to the infrared signals used to explain the difference between the samples: 2975 cm −1 , 2965 cm −1 , 2924 cm −1 and 2850 cm −1 . D: PCA-LDA in the spectral regions of 900–1280 cm −1 and 2800–3100 cm −1 on SR-FTIR spectra of the bacteria “pixels” from the chemical maps of the samples at the three different locations. On the right there is a plot of PCA-LDA loadings in the two spectral region of interest. PCA-LDA1 explains for the 54.5% of the variance, PCA-LDA2 for 28.6% and PCA-LDA3 for 7.3%. Arrows point to the main infrared signals used to explain the difference between the samples: 2958 cm −1 , 2925 cm −1 , 2870 cm −1 and 2850 cm −1 , in the second panel 1250 cm −1 , 1110 cm −1 , 1080 cm −1 and 1045 cm −1 .

Article Snippet: The PhyloChip G3 Assay (Second Genome, South San Francisco, CA) and analysis were carried out as described earlier .

Techniques:

Journal: American Journal of Rhinology & Allergy

Article Title: Microbiome of the paranasal sinuses: Update and literature review

doi: 10.2500/ajra.2016.30.4255

Figure Lengend Snippet: Steps involved in 16S rRNA sequencing. rRNA = ribosomal RNA; PCR = polymerase chain reaction.

Article Snippet: The 16S rRNA PhyloChip (Affymetrix Corporation, Santa Clara, CA) is a high-density phylogenetic microarray used for comparative analysis of bacterial community composition.

Techniques: Sequencing, Polymerase Chain Reaction