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  • 99
    Illumina Inc illumina miseq
    Next generation sequence analysis of pHW197-M. (A) Schematic representation of pHW197-M. HCMV: human cytomegalovirus promoter, T7: T7 RNA polymerase promoter, M1: matrix protein 1 open reading frame, M2: matrix protein 2 open reading frame (interrupted by an intron), hPolI: human RNA polymerase I promoter, pMB1 ori: origin of replication, Amp R : ampicillin resistance gene. (B) Mean sequencing depth after mapping the processed reads (n = 2) to the reference plasmid genome. The pHW197-M plasmid was fragmented with the Nextera XT DNA sample preparation kit before <t>Illumina</t> <t>MiSeq</t> sequence analysis or by Covaris mechanical shearing, followed by adaptor ligation before Ion Torrent PGM sequence analysis. (C) Percentage GC distribution in the pHW197-M plasmid reference sequence. The peak after position 2000 corresponds to the origin of replication.
    Illumina Miseq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 49861 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 49861 article reviews
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    99
    Illumina Inc miseq sequencing system
    Effects of OMO on the gut microbiota of the APP/PS1 transgenic mice, as determined from fecal samples. The rarefaction curve (A) , the results of the NMDS analysis (B) , PLS-DA results (C) , classification and abundance of fecal contents at the phylum level (D) , and the results of 16S rRNA sequencing of the gut microbiota using an <t>Illumina</t> <t>MiSeq</t> sequencing system are shown. N denotes the C57 group, M represents the APP/PS1 transgenic group, BD denotes the 50 mg/kg OMO-treated group, and BH indicates the 100 mg/kg OMO-treated group.
    Miseq Sequencing System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1375 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/miseq sequencing system/product/Illumina Inc
    Average 99 stars, based on 1375 article reviews
    Price from $9.99 to $1999.99
    miseq sequencing system - by Bioz Stars, 2020-07
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    89
    Illumina Inc illumina miseq sequence
    Taxonomic classification of water fungal community reads of <t>Illumina</t> <t>Miseq</t> data of ( A ) Lianhu lake (LL), ( B ) Xingqing lake (LX), and ( C ) Geming lake (LG) into phylum levels using the UNITE ( http://unite.ut.ee ) classifier database.
    Illumina Miseq Sequence, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 47 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq sequence/product/Illumina Inc
    Average 89 stars, based on 47 article reviews
    Price from $9.99 to $1999.99
    illumina miseq sequence - by Bioz Stars, 2020-07
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    Image Search Results


    Next generation sequence analysis of pHW197-M. (A) Schematic representation of pHW197-M. HCMV: human cytomegalovirus promoter, T7: T7 RNA polymerase promoter, M1: matrix protein 1 open reading frame, M2: matrix protein 2 open reading frame (interrupted by an intron), hPolI: human RNA polymerase I promoter, pMB1 ori: origin of replication, Amp R : ampicillin resistance gene. (B) Mean sequencing depth after mapping the processed reads (n = 2) to the reference plasmid genome. The pHW197-M plasmid was fragmented with the Nextera XT DNA sample preparation kit before Illumina MiSeq sequence analysis or by Covaris mechanical shearing, followed by adaptor ligation before Ion Torrent PGM sequence analysis. (C) Percentage GC distribution in the pHW197-M plasmid reference sequence. The peak after position 2000 corresponds to the origin of replication.

    Journal: BMC Genomics

    Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

    doi: 10.1186/s12864-015-1284-z

    Figure Lengend Snippet: Next generation sequence analysis of pHW197-M. (A) Schematic representation of pHW197-M. HCMV: human cytomegalovirus promoter, T7: T7 RNA polymerase promoter, M1: matrix protein 1 open reading frame, M2: matrix protein 2 open reading frame (interrupted by an intron), hPolI: human RNA polymerase I promoter, pMB1 ori: origin of replication, Amp R : ampicillin resistance gene. (B) Mean sequencing depth after mapping the processed reads (n = 2) to the reference plasmid genome. The pHW197-M plasmid was fragmented with the Nextera XT DNA sample preparation kit before Illumina MiSeq sequence analysis or by Covaris mechanical shearing, followed by adaptor ligation before Ion Torrent PGM sequence analysis. (C) Percentage GC distribution in the pHW197-M plasmid reference sequence. The peak after position 2000 corresponds to the origin of replication.

    Article Snippet: Nevertheless, the average quality (average Phred score) of the tracer mutations was higher on the Illumina MiSeq (37.97 ± 0.09) than on the Ion Torrent PGM (30.72 ± 1.07), making the detected variants on the Illumina MiSeq more reliable.

    Techniques: Sequencing, Plasmid Preparation, Sample Prep, Ligation

    Quality of sequencing reads obtained on the Illumina MiSeq and Ion Torrent PGM platforms. The pHW197-M and pHW197-Mmut plasmids (= 7) were fragmented with the Nextera XT DNA sample preparation kit (Illumina MiSeq) or with Covaris mechanical shearing followed by adaptor ligation (Ion Torrent PGM). Distribution of the read lengths obtained on the Illumina MiSeq (A) and Ion Torrent PGM (B) before processing (in black, output files of sequencer) and after processing (in orange) the obtained sequencing reads. Processing implies removal of adaptor contamination, quality trimming ( > Q20), the removal of ambiguous bases and removal of reads shorter than 50 bases. For the Illumina MiSeq reads, broken pairs after read processing were also removed during the processing. Error bars represent the standard deviation. (C, D) Per-base quality distribution of sequencing reads. The Phred score distribution (Y-axis) relative to the processed reads obtained after sequencing on the Illumina MiSeq (C) and Ion Torrent PGM (D) . x% ile = x th percentile of quality scores observed at that position.

    Journal: BMC Genomics

    Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

    doi: 10.1186/s12864-015-1284-z

    Figure Lengend Snippet: Quality of sequencing reads obtained on the Illumina MiSeq and Ion Torrent PGM platforms. The pHW197-M and pHW197-Mmut plasmids (= 7) were fragmented with the Nextera XT DNA sample preparation kit (Illumina MiSeq) or with Covaris mechanical shearing followed by adaptor ligation (Ion Torrent PGM). Distribution of the read lengths obtained on the Illumina MiSeq (A) and Ion Torrent PGM (B) before processing (in black, output files of sequencer) and after processing (in orange) the obtained sequencing reads. Processing implies removal of adaptor contamination, quality trimming ( > Q20), the removal of ambiguous bases and removal of reads shorter than 50 bases. For the Illumina MiSeq reads, broken pairs after read processing were also removed during the processing. Error bars represent the standard deviation. (C, D) Per-base quality distribution of sequencing reads. The Phred score distribution (Y-axis) relative to the processed reads obtained after sequencing on the Illumina MiSeq (C) and Ion Torrent PGM (D) . x% ile = x th percentile of quality scores observed at that position.

    Article Snippet: Nevertheless, the average quality (average Phred score) of the tracer mutations was higher on the Illumina MiSeq (37.97 ± 0.09) than on the Ion Torrent PGM (30.72 ± 1.07), making the detected variants on the Illumina MiSeq more reliable.

    Techniques: Sequencing, Sample Prep, Ligation, Standard Deviation

    Low frequency minor alleles are detected at significantly higher frequencies by Illumina MiSeq compared to Ion Torrent PGM. Nucleotide variants were subdivided in two frequency classes: high (frequency minor allele > 15%, n = 4) and low (frequency minor allele:

    Journal: BMC Genomics

    Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

    doi: 10.1186/s12864-015-1284-z

    Figure Lengend Snippet: Low frequency minor alleles are detected at significantly higher frequencies by Illumina MiSeq compared to Ion Torrent PGM. Nucleotide variants were subdivided in two frequency classes: high (frequency minor allele > 15%, n = 4) and low (frequency minor allele:

    Article Snippet: Nevertheless, the average quality (average Phred score) of the tracer mutations was higher on the Illumina MiSeq (37.97 ± 0.09) than on the Ion Torrent PGM (30.72 ± 1.07), making the detected variants on the Illumina MiSeq more reliable.

    Techniques:

    Coverage of PR8 virus genome with the optimized RT-PCR protocol. Sequence coverage for the different genome segments of wild type PR8 virus sequenced on Illumina MiSeq (2x250 bp) using two different fragmentation methods: Nextera XT transposase-based fragmentation (black lines) and mechanical Covaris shearing followed by adaptor ligation (orange lines). The obtained sequences were mapped to the reference genome (based on the plasmids used to generate the virus).

    Journal: BMC Genomics

    Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

    doi: 10.1186/s12864-015-1284-z

    Figure Lengend Snippet: Coverage of PR8 virus genome with the optimized RT-PCR protocol. Sequence coverage for the different genome segments of wild type PR8 virus sequenced on Illumina MiSeq (2x250 bp) using two different fragmentation methods: Nextera XT transposase-based fragmentation (black lines) and mechanical Covaris shearing followed by adaptor ligation (orange lines). The obtained sequences were mapped to the reference genome (based on the plasmids used to generate the virus).

    Article Snippet: Nevertheless, the average quality (average Phred score) of the tracer mutations was higher on the Illumina MiSeq (37.97 ± 0.09) than on the Ion Torrent PGM (30.72 ± 1.07), making the detected variants on the Illumina MiSeq more reliable.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Sequencing, Ligation

    Sequence coverage of the influenza virus genome. Sequence coverage for the different genome segments of wild type PR8 virus sequenced on Illumina MiSeq (2x250 bp, black lines, n = 2) or Ion Torrent PGM (Ion 318 chip v2, orange lines, n = 2). The obtained sequences were mapped to the reference genome (based on the pHW plasmids that were used to generate the virus, with addition of the extra 20 nucleotides present at the 5′ site in the RT-PCR primers).

    Journal: BMC Genomics

    Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

    doi: 10.1186/s12864-015-1284-z

    Figure Lengend Snippet: Sequence coverage of the influenza virus genome. Sequence coverage for the different genome segments of wild type PR8 virus sequenced on Illumina MiSeq (2x250 bp, black lines, n = 2) or Ion Torrent PGM (Ion 318 chip v2, orange lines, n = 2). The obtained sequences were mapped to the reference genome (based on the pHW plasmids that were used to generate the virus, with addition of the extra 20 nucleotides present at the 5′ site in the RT-PCR primers).

    Article Snippet: Nevertheless, the average quality (average Phred score) of the tracer mutations was higher on the Illumina MiSeq (37.97 ± 0.09) than on the Ion Torrent PGM (30.72 ± 1.07), making the detected variants on the Illumina MiSeq more reliable.

    Techniques: Sequencing, Chromatin Immunoprecipitation, Reverse Transcription Polymerase Chain Reaction

    Comparison of nucleotide variants revealed by Illumina MiSeq and Ion torrent PGM sequencing. The pHW197-M and pHW197-Mmut plasmids were fragmented with the Nextera XT DNA sample preparation kit (Illumina MiSeq) or by Covaris mechanical shearing, followed by adaptor ligation (Ion Torrent PGM). The samples were sequenced in duplicate and the sequence reads were processed (adaptor removal, Q20 trimming, removal of ambiguous bases and removal of reads shorter than 50 bases). For reads obtained on the Illumina MiSeq: broken pairs after read processing were also removed. The relative percentages of substitutions, insertions and deletions were determined after mapping the processed Illumina MiSeq (A) and Ion Torrent PGM (B) sequencing reads to the pHW197-M (n = 2) or pHW197-Mmut (n = 2) reference sequence. Bars represent averages from 4 samples and error bars represent the standard deviation.

    Journal: BMC Genomics

    Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

    doi: 10.1186/s12864-015-1284-z

    Figure Lengend Snippet: Comparison of nucleotide variants revealed by Illumina MiSeq and Ion torrent PGM sequencing. The pHW197-M and pHW197-Mmut plasmids were fragmented with the Nextera XT DNA sample preparation kit (Illumina MiSeq) or by Covaris mechanical shearing, followed by adaptor ligation (Ion Torrent PGM). The samples were sequenced in duplicate and the sequence reads were processed (adaptor removal, Q20 trimming, removal of ambiguous bases and removal of reads shorter than 50 bases). For reads obtained on the Illumina MiSeq: broken pairs after read processing were also removed. The relative percentages of substitutions, insertions and deletions were determined after mapping the processed Illumina MiSeq (A) and Ion Torrent PGM (B) sequencing reads to the pHW197-M (n = 2) or pHW197-Mmut (n = 2) reference sequence. Bars represent averages from 4 samples and error bars represent the standard deviation.

    Article Snippet: Nevertheless, the average quality (average Phred score) of the tracer mutations was higher on the Illumina MiSeq (37.97 ± 0.09) than on the Ion Torrent PGM (30.72 ± 1.07), making the detected variants on the Illumina MiSeq more reliable.

    Techniques: Sequencing, Sample Prep, Ligation, Standard Deviation

    Illustration of the process workflow. 1.) Cells are diluted in alginate polymer to a concentration of approximately 10 5 cells per microliter, resulting in a 10% occupancy rate in 100 μm microspheres. 2.) Cells are lysed using heat, and the bulk microsphere solids are mixed with reagents for a 2-step whole genome amplification reaction. 3.) After amplification, microspheres are diluted to extinction in a 384 well plate, and scanned for presence of single microspheres that fluoresce with PicoGreen DNA stain. 4.) An isolated microsphere is transferred to a fresh tube and the DNA products are recovered by dissolving the alginate matrix. These amplified products are submitted to further rounds of amplification to add sequencing adapters. 5.) The products are prepared for high throughput sequencing using the Illumina MiSeq platform. Intermediate steps include fluorescence microscopy and quantitative PCR for quality control.

    Journal: PLoS ONE

    Article Title: A Simple Method for Encapsulating Single Cells in Alginate Microspheres Allows for Direct PCR and Whole Genome Amplification

    doi: 10.1371/journal.pone.0117738

    Figure Lengend Snippet: Illustration of the process workflow. 1.) Cells are diluted in alginate polymer to a concentration of approximately 10 5 cells per microliter, resulting in a 10% occupancy rate in 100 μm microspheres. 2.) Cells are lysed using heat, and the bulk microsphere solids are mixed with reagents for a 2-step whole genome amplification reaction. 3.) After amplification, microspheres are diluted to extinction in a 384 well plate, and scanned for presence of single microspheres that fluoresce with PicoGreen DNA stain. 4.) An isolated microsphere is transferred to a fresh tube and the DNA products are recovered by dissolving the alginate matrix. These amplified products are submitted to further rounds of amplification to add sequencing adapters. 5.) The products are prepared for high throughput sequencing using the Illumina MiSeq platform. Intermediate steps include fluorescence microscopy and quantitative PCR for quality control.

    Article Snippet: This quantity of DNA is six orders of magnitude less material than required for the current Illumina MiSeq platform.

    Techniques: Concentration Assay, Whole Genome Amplification, Amplification, Staining, Isolation, Sequencing, Next-Generation Sequencing, Fluorescence, Microscopy, Real-time Polymerase Chain Reaction

    Fecal microbiota analysis in a patient with cap polyposis. (A) Stool samples were obtained from a patient with cap polyposis prior to, 1 week and 6 months post-antibiotic treatment. DNA samples extracted from the stool specimens were subjected to polymerase chain reaction for the amplification of the 16S ribosomal RNA (16S rRNA) V3 and V4 regions. We performed 16S rRNA sequencing using the MiSeq system. The relative abundance of different bacterial taxa at the genus level in each sample has been shown. (B) Comparative analysis of the taxonomic composition of the fecal microbial community at the genus level. Relative abundance of the genera has been shown as a percentage.

    Journal: Frontiers in Immunology

    Article Title: Dysbiosis-Associated Polyposis of the Colon—Cap Polyposis

    doi: 10.3389/fimmu.2018.00918

    Figure Lengend Snippet: Fecal microbiota analysis in a patient with cap polyposis. (A) Stool samples were obtained from a patient with cap polyposis prior to, 1 week and 6 months post-antibiotic treatment. DNA samples extracted from the stool specimens were subjected to polymerase chain reaction for the amplification of the 16S ribosomal RNA (16S rRNA) V3 and V4 regions. We performed 16S rRNA sequencing using the MiSeq system. The relative abundance of different bacterial taxa at the genus level in each sample has been shown. (B) Comparative analysis of the taxonomic composition of the fecal microbial community at the genus level. Relative abundance of the genera has been shown as a percentage.

    Article Snippet: We performed 16S rRNA sequencing using the MiSeq system (Illumina) ( , ).

    Techniques: Polymerase Chain Reaction, Amplification, Sequencing

    Overview of the sequencing assay used to characterize blood meal composition of individual mosquitoes. (i) A first PCR amplification is performed on DNA extracted from each mosquito targeting ~140 bp of the mammalian mt 16S rRNA (gray) using primers modified with a 5’-end tail complementary to the Illumina sequencing primers (red). (ii) A second PCR amplification incorporates the Illumina adaptors and a 6-nucleotide barcode unique to each mosquito at the ends of the individual blood meal PCR products. (iii) After pooling amplification products from 96 samples together, the PCR products are simultaneously sequenced on an Illumina MiSeq to (iv) generate paired-end reads (in grey) and barcode sequences (grey box). (v) Paired-end reads are then merged to provide error-corrected consensus sequence reads. The dotted black line indicates that the 6-nucleotide barcode corresponding to each read is known but is sequenced independently.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing

    doi: 10.1371/journal.pntd.0004512

    Figure Lengend Snippet: Overview of the sequencing assay used to characterize blood meal composition of individual mosquitoes. (i) A first PCR amplification is performed on DNA extracted from each mosquito targeting ~140 bp of the mammalian mt 16S rRNA (gray) using primers modified with a 5’-end tail complementary to the Illumina sequencing primers (red). (ii) A second PCR amplification incorporates the Illumina adaptors and a 6-nucleotide barcode unique to each mosquito at the ends of the individual blood meal PCR products. (iii) After pooling amplification products from 96 samples together, the PCR products are simultaneously sequenced on an Illumina MiSeq to (iv) generate paired-end reads (in grey) and barcode sequences (grey box). (v) Paired-end reads are then merged to provide error-corrected consensus sequence reads. The dotted black line indicates that the 6-nucleotide barcode corresponding to each read is known but is sequenced independently.

    Article Snippet: We characterized the blood meal composition of a total of 442 female Anopheles by amplifying the mammalian mt 16S rRNA genes from DNA extracted from these mosquitoes, pooling the PCR products of 96 samples after individual barcoding, and simultaneously sequencing the samples on an Illumina MiSeq instrument ( ).

    Techniques: Sequencing, Polymerase Chain Reaction, Amplification, Modification

    Plasmodium vivax chromosomal coverage following SWGA using primer set pvset1 (A) or pvset1920 (B). The base compositions of chromosomes 2 and 6 were visualized in Geneious (version 9.1) using the P. vivax Sal-1 reference genome; green and blue lines represent percentages of AT and GC content, respectively, plotted for 25-bp windows across the chromosome (scale shown above the graph). Shown in blue and red below are the corresponding MiSeq read coverage depths using primer sets pvset1 and pvset1920, respectively. Coverage plots were generated using IGVTools (version 2.3.40) and are shown on a log scale with maximum read depth indicated in the upper left corner of the plot.

    Journal: mBio

    Article Title: Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples

    doi: 10.1128/mBio.02257-16

    Figure Lengend Snippet: Plasmodium vivax chromosomal coverage following SWGA using primer set pvset1 (A) or pvset1920 (B). The base compositions of chromosomes 2 and 6 were visualized in Geneious (version 9.1) using the P. vivax Sal-1 reference genome; green and blue lines represent percentages of AT and GC content, respectively, plotted for 25-bp windows across the chromosome (scale shown above the graph). Shown in blue and red below are the corresponding MiSeq read coverage depths using primer sets pvset1 and pvset1920, respectively. Coverage plots were generated using IGVTools (version 2.3.40) and are shown on a log scale with maximum read depth indicated in the upper left corner of the plot.

    Article Snippet: 10.1128/mBio.02257-16.1 FIG S1 Testing of SWGA primer sets on an unprocessed, P. vivax -infected blood sample. (A) Unamplified DNA (black) and DNA amplified with SWGA primer set pvset1 (blue) was sequenced on a MiSeq (Illumina).

    Techniques: Generated

    Testing of SWGA primer sets on DNA from an unprocessed, P. vivax -infected blood sample. (A) Unamplified DNA (black) and DNA amplified with SWGA primer set pvset1 (blue) or pvset1920 (red) was sequenced on a MiSeq (Illumina). The percentages of MiSeq reads that mapped to the P. vivax Sal-1 reference genome in Geneious (version 9.1) ( 39 ) were plotted for both unamplified and SWGA-amplified samples. (B) The 1× P. vivax genome coverage is shown relative to the total sequencing depth (in millions of base pairs sequenced) for samples subjected to SWGA with pvset1920 or pvset1 and for unamplified DNA.

    Journal: mBio

    Article Title: Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples

    doi: 10.1128/mBio.02257-16

    Figure Lengend Snippet: Testing of SWGA primer sets on DNA from an unprocessed, P. vivax -infected blood sample. (A) Unamplified DNA (black) and DNA amplified with SWGA primer set pvset1 (blue) or pvset1920 (red) was sequenced on a MiSeq (Illumina). The percentages of MiSeq reads that mapped to the P. vivax Sal-1 reference genome in Geneious (version 9.1) ( 39 ) were plotted for both unamplified and SWGA-amplified samples. (B) The 1× P. vivax genome coverage is shown relative to the total sequencing depth (in millions of base pairs sequenced) for samples subjected to SWGA with pvset1920 or pvset1 and for unamplified DNA.

    Article Snippet: 10.1128/mBio.02257-16.1 FIG S1 Testing of SWGA primer sets on an unprocessed, P. vivax -infected blood sample. (A) Unamplified DNA (black) and DNA amplified with SWGA primer set pvset1 (blue) was sequenced on a MiSeq (Illumina).

    Techniques: Infection, Amplification, Sequencing

    Annotated OTUs per platform at all taxonomic levels. Percentage (%) of annotated OTUs on each taxonomic level for both Illumina MiSeq (MiSeq) and Ion Torrent PGM (IT) sequencing platforms.

    Journal: Scientific Reports

    Article Title: Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies

    doi: 10.1038/s41598-018-23296-4

    Figure Lengend Snippet: Annotated OTUs per platform at all taxonomic levels. Percentage (%) of annotated OTUs on each taxonomic level for both Illumina MiSeq (MiSeq) and Ion Torrent PGM (IT) sequencing platforms.

    Article Snippet: Faecal bacterial communities were profiled by 16S rRNA amplicon sequencing using two NGS platforms: Illumina MiSeq (MiSeq) and Ion Torrent PGM (IT).

    Techniques: Sequencing

    PR8-induced IFN-Is alter the fecal microbiota composition, Analysis of fecal microbiota in WT and Ifnar1 -/- mice performed by MiSeq and 16S qPCR during influenza infection. A) Experimental model. Fecal samples were collected from mice on day 0 before infection and on day 9 after mock and PR8 infection. Mice were euthanized at 17 dpi. B, C) The fecal microbiota from WT and Ifnar1 -/- mice on day 0 before infection (n = 6 WT, n = 6 Ifnar1 -/- ), and on day 9 after mock (n = 3 WT, n = 3 Ifnar1 -/- ) and PR8 infection (n = 3 WT, n = 3 Ifnar1 -/- ) was analyzed by sequencing using the Illumina MiSeq system. Graphed is the average relative abundance of each bacterial phylum (B) and genus (C); the cut-off abundance level was set at 0.5%. D) Analysis of the fecal Enterobacteriaceae using 16S qPCR. Fecal samples were collected from mice on day 0 before infection (n = 10 WT, n = 8 Ifnar1 -/- ) and on day 9 after mock (n = 5 WT, n = 4 Ifnar1 -/- ) and PR8 infection (n = 5 WT, n = 4 Ifnar1 -/- ). Copy numbers of Enterobacteriaceae per μl of fecal microbial DNA is shown. Each dot represents one mouse, the geometric mean is indicated. P values were calculated by One-Way ANOVA (Bonferroni multiple comparison test). ***p

    Journal: PLoS Pathogens

    Article Title: Influenza Virus Affects Intestinal Microbiota and Secondary Salmonella Infection in the Gut through Type I Interferons

    doi: 10.1371/journal.ppat.1005572

    Figure Lengend Snippet: PR8-induced IFN-Is alter the fecal microbiota composition, Analysis of fecal microbiota in WT and Ifnar1 -/- mice performed by MiSeq and 16S qPCR during influenza infection. A) Experimental model. Fecal samples were collected from mice on day 0 before infection and on day 9 after mock and PR8 infection. Mice were euthanized at 17 dpi. B, C) The fecal microbiota from WT and Ifnar1 -/- mice on day 0 before infection (n = 6 WT, n = 6 Ifnar1 -/- ), and on day 9 after mock (n = 3 WT, n = 3 Ifnar1 -/- ) and PR8 infection (n = 3 WT, n = 3 Ifnar1 -/- ) was analyzed by sequencing using the Illumina MiSeq system. Graphed is the average relative abundance of each bacterial phylum (B) and genus (C); the cut-off abundance level was set at 0.5%. D) Analysis of the fecal Enterobacteriaceae using 16S qPCR. Fecal samples were collected from mice on day 0 before infection (n = 10 WT, n = 8 Ifnar1 -/- ) and on day 9 after mock (n = 5 WT, n = 4 Ifnar1 -/- ) and PR8 infection (n = 5 WT, n = 4 Ifnar1 -/- ). Copy numbers of Enterobacteriaceae per μl of fecal microbial DNA is shown. Each dot represents one mouse, the geometric mean is indicated. P values were calculated by One-Way ANOVA (Bonferroni multiple comparison test). ***p

    Article Snippet: Libraries were sequenced using an Illumina MiSeq system.

    Techniques: Mouse Assay, Real-time Polymerase Chain Reaction, Infection, Sequencing

    Relative abundances (%) of bacterial community in the analyzed samples identified by analysis of V3-V4 region of the 16S rRNA gene through MiSeq Illumina. C, coffee by-product; HC, H . illucens reared on coffee by-product; HCF, frass of H . illucens reared on coffee by-product; S, vegetable substrate; HS, H . illucens reared on vegetable substrate; HSF, frass of H . illucens reared on vegetable substrate; ZHC, gut content of zebrafish fed HC; ZHS, gut content of zebrafish fed HS.

    Journal: PLoS ONE

    Article Title: Hermetia illucens in diets for zebrafish (Danio rerio): A study of bacterial diversity by using PCR-DGGE and metagenomic sequencing

    doi: 10.1371/journal.pone.0225956

    Figure Lengend Snippet: Relative abundances (%) of bacterial community in the analyzed samples identified by analysis of V3-V4 region of the 16S rRNA gene through MiSeq Illumina. C, coffee by-product; HC, H . illucens reared on coffee by-product; HCF, frass of H . illucens reared on coffee by-product; S, vegetable substrate; HS, H . illucens reared on vegetable substrate; HSF, frass of H . illucens reared on vegetable substrate; ZHC, gut content of zebrafish fed HC; ZHS, gut content of zebrafish fed HS.

    Article Snippet: Raw data of relative abundances (%) of bacterial community in the analyzed samples identified by analysis of V3-V4 region of the 16S rRNA gene by using MiSeq Illumina. (XLSX) Click here for additional data file.

    Techniques:

    Alteration of fecal bacterial communities in Opn KO mice. Eight-week-old female Opn KO and WT mice were co-housed for 3 weeks prior to collection of feces and extraction of DNA. These mice were bred and maintained in the same facility for at least three generations. Illumina MiSeq analysis of 16S rRNA was then performed. Data are from (a) each sample and (b) the average of the groups. Data was normalized against common bacterial 16S rRNA expression and is presented as a ratio to the value obtained in WT mice (n = 5, per group).

    Journal: PLoS ONE

    Article Title: The potential role of Osteopontin in the maintenance of commensal bacteria homeostasis in the intestine

    doi: 10.1371/journal.pone.0173629

    Figure Lengend Snippet: Alteration of fecal bacterial communities in Opn KO mice. Eight-week-old female Opn KO and WT mice were co-housed for 3 weeks prior to collection of feces and extraction of DNA. These mice were bred and maintained in the same facility for at least three generations. Illumina MiSeq analysis of 16S rRNA was then performed. Data are from (a) each sample and (b) the average of the groups. Data was normalized against common bacterial 16S rRNA expression and is presented as a ratio to the value obtained in WT mice (n = 5, per group).

    Article Snippet: To examine whether Opn-producing cells play a role in the homeostasis of commensal microflora, we examined the composition of intestinal bacteria using Illumina MiSeq analysis of DNA extracted from fecal samples collected from co-housed WT and Opn KO mice.

    Techniques: Mouse Assay, Expressing

    a Comparison of beta diversity results for the mock bacterial community and the healthy volunteer skin samples sequenced on both Roche 454 and Illumina MiSeq using Procrustes plot comparing the principal co-ordinates of Bray-Curtis distances. b Comparison of beta diversity results for the mock bacterial community and the healthy volunteer skin samples sequenced on both Roche 454 and Illumina MiSeq using Procrustes plot comparing the principal co-ordinates of Unweighted UniFrac distances. Lines connect paired sample sequences on the Roche454 ( white tip of line ) and Illumina Miseq ( red tip of line )

    Journal: BMC Microbiology

    Article Title: Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform

    doi: 10.1186/s12866-017-0927-4

    Figure Lengend Snippet: a Comparison of beta diversity results for the mock bacterial community and the healthy volunteer skin samples sequenced on both Roche 454 and Illumina MiSeq using Procrustes plot comparing the principal co-ordinates of Bray-Curtis distances. b Comparison of beta diversity results for the mock bacterial community and the healthy volunteer skin samples sequenced on both Roche 454 and Illumina MiSeq using Procrustes plot comparing the principal co-ordinates of Unweighted UniFrac distances. Lines connect paired sample sequences on the Roche454 ( white tip of line ) and Illumina Miseq ( red tip of line )

    Article Snippet: The mock bacterial community had an SW diversity index (n = 4 for each platform) of 1.85 and 2 for the Roche 454 Junior and the Illumina MiSeq platforms, respectively, when calculated based on the genus level distribution (Fig.

    Techniques:

    High-throughput workflow for the preparation of plasmid DNA libraries for NGS. Plasmid DNA samples are isolated from bacteria cells using a high-throughput plasmid isolation method on the CyBio ® FeliX robot. All steps performed using the FeliX platform are highlighted with a grey outline. The isolated plasmid samples are tested for the presence of genomic DNA (gDNA), prior to library preparation, using the Labcyte Echo ® . All steps performed using the Labcyte Echo ® are highlighted with a shaded grey box. If samples are free from gDNA, they are diluted to 0.4 ng/μl in H 2 O. If gDNA is detected, the samples are sonicated prior to re-testing in the gDNA QC assay. Using reagents from the Nextera XT kit, a tagmentation reaction is performed on all samples under the optimised conditions, followed by neutralization of the reaction. Unique combinations of index primers are added to all samples via 12 PCR cycles, followed by magnetic bead purification of the PCR products. The concentration of the purified dsDNA is then determined using the PicoGreen ® reagent assay and the libraries are pooled to give a final concentration of 4–10 nM, in a minimum volume of 15 μl. The average fragment size of the pooled libraries is measured using the Fragment Analyzer before being sequenced on the Illumina ® MiSeq system.

    Journal: Synthetic and Systems Biotechnology

    Article Title: Miniaturisation of high-throughput plasmid DNA library preparation for next-generation sequencing using multifactorial optimisation

    doi: 10.1016/j.synbio.2019.01.002

    Figure Lengend Snippet: High-throughput workflow for the preparation of plasmid DNA libraries for NGS. Plasmid DNA samples are isolated from bacteria cells using a high-throughput plasmid isolation method on the CyBio ® FeliX robot. All steps performed using the FeliX platform are highlighted with a grey outline. The isolated plasmid samples are tested for the presence of genomic DNA (gDNA), prior to library preparation, using the Labcyte Echo ® . All steps performed using the Labcyte Echo ® are highlighted with a shaded grey box. If samples are free from gDNA, they are diluted to 0.4 ng/μl in H 2 O. If gDNA is detected, the samples are sonicated prior to re-testing in the gDNA QC assay. Using reagents from the Nextera XT kit, a tagmentation reaction is performed on all samples under the optimised conditions, followed by neutralization of the reaction. Unique combinations of index primers are added to all samples via 12 PCR cycles, followed by magnetic bead purification of the PCR products. The concentration of the purified dsDNA is then determined using the PicoGreen ® reagent assay and the libraries are pooled to give a final concentration of 4–10 nM, in a minimum volume of 15 μl. The average fragment size of the pooled libraries is measured using the Fragment Analyzer before being sequenced on the Illumina ® MiSeq system.

    Article Snippet: 3.3 Optimisation of plasmid DNA library preparation for NGS using Design of Experiments For sequencing of plasmid DNA using the Illumina ® MiSeq platform, a library of fragments with a mean size of between 200 and 400 bp, each with a concentration of 0.5–5 ng/μl is required.

    Techniques: High Throughput Screening Assay, Plasmid Preparation, Next-Generation Sequencing, Isolation, Sonication, Neutralization, Polymerase Chain Reaction, Purification, Concentration Assay

    Next generation sequencing of plasmid DNA libraries, prepared using a miniaturised method with the Nextera XT library preparation kit. 96 plasmid DNA libraries were prepared for NGS with the Nextera XT library preparation kit, using optimised conditions (12.5 min incubation, 50 nl sample, 1.8x magnetic bead solution). ( A ) After purification, the samples were quantified in the PicoGreen ® dsDNA quantification assay. The data show that 75/92 samples have a concentration within the desired range (0.5–5 ng/μl), with an average concentration of 1.1 ng/μl. These samples were pooled, with a final concentration of 6.64 nM and run on the Fragment Analyzer ( B ) and ( C ). All fragments in the pooled libraries are of the desired size (200–400 bp). ( D ) The pooled library was sequenced on the Illumina ® MiSeq system (2 × 150 method). The mean sequence quality (Phred) scores are plotted for each sample. For all samples, the sequence quality (Phred) score was > 30 for more than 85% of the base pairs, indicating that all samples passed the QC criteria.

    Journal: Synthetic and Systems Biotechnology

    Article Title: Miniaturisation of high-throughput plasmid DNA library preparation for next-generation sequencing using multifactorial optimisation

    doi: 10.1016/j.synbio.2019.01.002

    Figure Lengend Snippet: Next generation sequencing of plasmid DNA libraries, prepared using a miniaturised method with the Nextera XT library preparation kit. 96 plasmid DNA libraries were prepared for NGS with the Nextera XT library preparation kit, using optimised conditions (12.5 min incubation, 50 nl sample, 1.8x magnetic bead solution). ( A ) After purification, the samples were quantified in the PicoGreen ® dsDNA quantification assay. The data show that 75/92 samples have a concentration within the desired range (0.5–5 ng/μl), with an average concentration of 1.1 ng/μl. These samples were pooled, with a final concentration of 6.64 nM and run on the Fragment Analyzer ( B ) and ( C ). All fragments in the pooled libraries are of the desired size (200–400 bp). ( D ) The pooled library was sequenced on the Illumina ® MiSeq system (2 × 150 method). The mean sequence quality (Phred) scores are plotted for each sample. For all samples, the sequence quality (Phred) score was > 30 for more than 85% of the base pairs, indicating that all samples passed the QC criteria.

    Article Snippet: 3.3 Optimisation of plasmid DNA library preparation for NGS using Design of Experiments For sequencing of plasmid DNA using the Illumina ® MiSeq platform, a library of fragments with a mean size of between 200 and 400 bp, each with a concentration of 0.5–5 ng/μl is required.

    Techniques: Next-Generation Sequencing, Plasmid Preparation, Incubation, Purification, Concentration Assay, Sequencing

    —Examples of sequence alignments between Bemisia tabaci “Peru” MEAM1 mtDNA COI haplotype gene region, published “MEAM2” mtDNA COI gene region, and NGS candidate NUMT sequences identified from KX234913, KY951449, and the KY951452 individuals. ( A ) C-terminal region of a Peruvian MEAM1 B. tabaci (KY951450) mtDNA COI gene region showing putative stop codon (black shaded “*” symbol), as well as the B. tabaci “MEAM2” haplotype from Japan (AJ550177), and examples NGS candidate NUMT sequences from the Peruvian B. tabaci MEAM1 (KX234914) with matching SNPs (indicated by red boxes) that matched the Japan MEAM2 haplotype (AJ550177). Deletion of a “T” base (indicated by red triangle) resulted in a frameshift mutation and the loss of the putative mtDNA COI gene stop codon. ( B ) Internal stop codons (at positions 904S906) detected in candidate NUMT sequences (KY951452_NUMT-01, KY951452_NUMT-02) from the Peruvian MEAM1 individual (KY951452) MiSeq generated DNA fragments when compared with the Peruvian B. tabaci MEAM1 (KX234914) mtDNA COI gene. Stop codons detected in NUMT sequences were the result of a single nucleotide base change at position 906 from a “T” to an “A.” Candidate NUMT sequences were also compared with the Peruvian MEAM2 haplotype (KY951454) obtained via PCR and Sanger sequencing of the same MEAM1 individual (KY951452). Nucleotide positions based on the mtDNA COI gene are provided. Amino acid translation based on the invertebrate mitochondrial genetic codes (Translational Table_5). Significant changes between amino acids are highlighted.

    Journal: Genome Biology and Evolution

    Article Title: The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Complex

    doi: 10.1093/gbe/evx173

    Figure Lengend Snippet: —Examples of sequence alignments between Bemisia tabaci “Peru” MEAM1 mtDNA COI haplotype gene region, published “MEAM2” mtDNA COI gene region, and NGS candidate NUMT sequences identified from KX234913, KY951449, and the KY951452 individuals. ( A ) C-terminal region of a Peruvian MEAM1 B. tabaci (KY951450) mtDNA COI gene region showing putative stop codon (black shaded “*” symbol), as well as the B. tabaci “MEAM2” haplotype from Japan (AJ550177), and examples NGS candidate NUMT sequences from the Peruvian B. tabaci MEAM1 (KX234914) with matching SNPs (indicated by red boxes) that matched the Japan MEAM2 haplotype (AJ550177). Deletion of a “T” base (indicated by red triangle) resulted in a frameshift mutation and the loss of the putative mtDNA COI gene stop codon. ( B ) Internal stop codons (at positions 904S906) detected in candidate NUMT sequences (KY951452_NUMT-01, KY951452_NUMT-02) from the Peruvian MEAM1 individual (KY951452) MiSeq generated DNA fragments when compared with the Peruvian B. tabaci MEAM1 (KX234914) mtDNA COI gene. Stop codons detected in NUMT sequences were the result of a single nucleotide base change at position 906 from a “T” to an “A.” Candidate NUMT sequences were also compared with the Peruvian MEAM2 haplotype (KY951454) obtained via PCR and Sanger sequencing of the same MEAM1 individual (KY951452). Nucleotide positions based on the mtDNA COI gene are provided. Amino acid translation based on the invertebrate mitochondrial genetic codes (Translational Table_5). Significant changes between amino acids are highlighted.

    Article Snippet: We identified low copy genome fragments through the Illumina MiSeq sequencing platform in MEAM1 individuals that matched unique MEAM2 SNPs ( ).

    Techniques: Sequencing, Next-Generation Sequencing, Mutagenesis, Generated, Polymerase Chain Reaction

    Effects of OMO on the gut microbiota of the APP/PS1 transgenic mice, as determined from fecal samples. The rarefaction curve (A) , the results of the NMDS analysis (B) , PLS-DA results (C) , classification and abundance of fecal contents at the phylum level (D) , and the results of 16S rRNA sequencing of the gut microbiota using an Illumina MiSeq sequencing system are shown. N denotes the C57 group, M represents the APP/PS1 transgenic group, BD denotes the 50 mg/kg OMO-treated group, and BH indicates the 100 mg/kg OMO-treated group.

    Journal: Frontiers in Neurology

    Article Title: Effects of Oligosaccharides From Morinda officinalis on Gut Microbiota and Metabolome of APP/PS1 Transgenic Mice

    doi: 10.3389/fneur.2018.00412

    Figure Lengend Snippet: Effects of OMO on the gut microbiota of the APP/PS1 transgenic mice, as determined from fecal samples. The rarefaction curve (A) , the results of the NMDS analysis (B) , PLS-DA results (C) , classification and abundance of fecal contents at the phylum level (D) , and the results of 16S rRNA sequencing of the gut microbiota using an Illumina MiSeq sequencing system are shown. N denotes the C57 group, M represents the APP/PS1 transgenic group, BD denotes the 50 mg/kg OMO-treated group, and BH indicates the 100 mg/kg OMO-treated group.

    Article Snippet: An Illumina MiSeq sequencing system was utilized to sequence 20 mL of the pooled admixture.

    Techniques: Transgenic Assay, Mouse Assay, Sequencing

    Taxonomic classification of water fungal community reads of Illumina Miseq data of ( A ) Lianhu lake (LL), ( B ) Xingqing lake (LX), and ( C ) Geming lake (LG) into phylum levels using the UNITE ( http://unite.ut.ee ) classifier database.

    Journal: International Journal of Environmental Research and Public Health

    Article Title: Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi’an, China

    doi: 10.3390/ijerph15030469

    Figure Lengend Snippet: Taxonomic classification of water fungal community reads of Illumina Miseq data of ( A ) Lianhu lake (LL), ( B ) Xingqing lake (LX), and ( C ) Geming lake (LG) into phylum levels using the UNITE ( http://unite.ut.ee ) classifier database.

    Article Snippet: The specific aims of present study are: (1) to assess the general water quality parameters; (2) to reveal morphological features of water microbial community using scanning electron microscopy (SEM); (3) to determine the functional diversity of water bacterial communities based on community level physiological profiles (CLPPs) as well as water bacterial and fungal community compositions using 16S rRNA and Internal Transcribed Spacer (ITS) genes in the Illumina Miseq sequence in LX, LG and LL urban lakes; and (4) to investigate the relationship between water quality and microbial community structure.

    Techniques:

    Taxonomic classification of water bacterial community reads of Illumina Miseq sequencing data of ( A ) Lianhu lake (LL), ( B ) Xingqing lake (LX), and ( C ) Geming lake (LG) into phylum levels using the Ribosomal Database Project (RDP) classifier.

    Journal: International Journal of Environmental Research and Public Health

    Article Title: Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi’an, China

    doi: 10.3390/ijerph15030469

    Figure Lengend Snippet: Taxonomic classification of water bacterial community reads of Illumina Miseq sequencing data of ( A ) Lianhu lake (LL), ( B ) Xingqing lake (LX), and ( C ) Geming lake (LG) into phylum levels using the Ribosomal Database Project (RDP) classifier.

    Article Snippet: The specific aims of present study are: (1) to assess the general water quality parameters; (2) to reveal morphological features of water microbial community using scanning electron microscopy (SEM); (3) to determine the functional diversity of water bacterial communities based on community level physiological profiles (CLPPs) as well as water bacterial and fungal community compositions using 16S rRNA and Internal Transcribed Spacer (ITS) genes in the Illumina Miseq sequence in LX, LG and LL urban lakes; and (4) to investigate the relationship between water quality and microbial community structure.

    Techniques: Sequencing

    Water bacterial ( A ) and fungal ( B ) community operational taxonomic units (OTUs) number at 0.97 level and the reads number sampled based on Illumina Miseq data of Geming lake (LG), Lianhu lake (LL), and Xingqing lake (LX) in Xi’an City, Shaanxi Province, China.

    Journal: International Journal of Environmental Research and Public Health

    Article Title: Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi’an, China

    doi: 10.3390/ijerph15030469

    Figure Lengend Snippet: Water bacterial ( A ) and fungal ( B ) community operational taxonomic units (OTUs) number at 0.97 level and the reads number sampled based on Illumina Miseq data of Geming lake (LG), Lianhu lake (LL), and Xingqing lake (LX) in Xi’an City, Shaanxi Province, China.

    Article Snippet: The specific aims of present study are: (1) to assess the general water quality parameters; (2) to reveal morphological features of water microbial community using scanning electron microscopy (SEM); (3) to determine the functional diversity of water bacterial communities based on community level physiological profiles (CLPPs) as well as water bacterial and fungal community compositions using 16S rRNA and Internal Transcribed Spacer (ITS) genes in the Illumina Miseq sequence in LX, LG and LL urban lakes; and (4) to investigate the relationship between water quality and microbial community structure.

    Techniques: