miseq platform  (Illumina Inc)

 
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    MiSeq System
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    Structured Review

    Illumina Inc miseq platform
    MiSeq System

    https://www.bioz.com/result/miseq platform/product/Illumina Inc
    Average 99 stars, based on 20 article reviews
    Price from $9.99 to $1999.99
    miseq platform - by Bioz Stars, 2020-07
    99/100 stars

    Images

    1) Product Images from "Miniaturisation of high-throughput plasmid DNA library preparation for next-generation sequencing using multifactorial optimisation"

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

    Journal: Synthetic and Systems Biotechnology

    doi: 10.1016/j.synbio.2019.01.002

    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.
    Figure Legend 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.

    Techniques Used: 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.
    Figure Legend 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.

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

    2) Product Images from "MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species"

    Article Title: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

    Journal: Royal Society Open Science

    doi: 10.1098/rsos.150088

    Schematic representation of the paired-end library preparation using a two-step tailed PCR. The workflow is derived from a document ‘16S metagenomic sequencing library preparation: preparing 16S ribosomal gene amplicons for the Illumina MiSeq system’ distributed by Illumina (part no. 15044223 Rev. B) and the figure was drawn with reference to a website of the Genomics and Sequencing Center at the University of Rhode Island ( http://web.uri.edu/gsc/next-generation-sequencing/ ).
    Figure Legend Snippet: Schematic representation of the paired-end library preparation using a two-step tailed PCR. The workflow is derived from a document ‘16S metagenomic sequencing library preparation: preparing 16S ribosomal gene amplicons for the Illumina MiSeq system’ distributed by Illumina (part no. 15044223 Rev. B) and the figure was drawn with reference to a website of the Genomics and Sequencing Center at the University of Rhode Island ( http://web.uri.edu/gsc/next-generation-sequencing/ ).

    Techniques Used: Polymerase Chain Reaction, Derivative Assay, Sequencing, Next-Generation Sequencing

    3) Product Images from "The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces"

    Article Title: The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces

    Journal: Scientific Data

    doi: 10.1038/sdata.2018.68

    Relationship between sequence read length and assignment to database. ( a and b ) Sequences ( n =10,000) covering the V1–4 (red), V1–3 (light blue), V3–4 (blue), V4 (dark blue), and V1–9 (green) regions of the 16 S rRNA gene were extracted in silico from the GG 16 S rRNA gene database. ( a ) Pairwise similarities between targeted regions are represented as similarity distributions (lower left), similarity histograms (diagonal), and correlation coefficient values (upper right). ( b ) Accuracy of phylogenetic reconstruction per targeted region. Precision (x-axis) and recall (y-axis) were calculated based on 100 randomly chosen bootstrap replications. ( c ) Distribution of sequence (30,000 sub-sampled) similarities, including and excluding indel errors, between data generated by GS FLX+, Illumina MiSeq, and PacBio, and data from publically available PacBio sequences.
    Figure Legend Snippet: Relationship between sequence read length and assignment to database. ( a and b ) Sequences ( n =10,000) covering the V1–4 (red), V1–3 (light blue), V3–4 (blue), V4 (dark blue), and V1–9 (green) regions of the 16 S rRNA gene were extracted in silico from the GG 16 S rRNA gene database. ( a ) Pairwise similarities between targeted regions are represented as similarity distributions (lower left), similarity histograms (diagonal), and correlation coefficient values (upper right). ( b ) Accuracy of phylogenetic reconstruction per targeted region. Precision (x-axis) and recall (y-axis) were calculated based on 100 randomly chosen bootstrap replications. ( c ) Distribution of sequence (30,000 sub-sampled) similarities, including and excluding indel errors, between data generated by GS FLX+, Illumina MiSeq, and PacBio, and data from publically available PacBio sequences.

    Techniques Used: Sequencing, In Silico, Generated

    Taxonomy profiles in each platform-generated datasets. ( a ) The proportion of assigned sequences from the GS FLX+ ( n =169, red), MiSeq V4 ( n =169, blue), and PacBio ( n =29, green) datasets was determined by assigning the sequences to the GG 16 S rRNA gene sequence database, and are represented at the family, genus, and species levels. ( b ) The abundance patterns of bacterial taxa in each dataset were analyzed using the linear discriminant analysis effect size (LEfSe) circular cladogram. The discriminant taxa for the GS FLX+, MiSeq V4, and PacBio datasets are shown in red, blue, and green, respectively. ( c ) Relative abundances of the phylum Bacteroidetes , Actinobacteria and Proteobacteria in OTU tables for each dataset are represented as bar graphs. Data were analyzed by ANOVA followed by Tukey’s post hoc test (* P
    Figure Legend Snippet: Taxonomy profiles in each platform-generated datasets. ( a ) The proportion of assigned sequences from the GS FLX+ ( n =169, red), MiSeq V4 ( n =169, blue), and PacBio ( n =29, green) datasets was determined by assigning the sequences to the GG 16 S rRNA gene sequence database, and are represented at the family, genus, and species levels. ( b ) The abundance patterns of bacterial taxa in each dataset were analyzed using the linear discriminant analysis effect size (LEfSe) circular cladogram. The discriminant taxa for the GS FLX+, MiSeq V4, and PacBio datasets are shown in red, blue, and green, respectively. ( c ) Relative abundances of the phylum Bacteroidetes , Actinobacteria and Proteobacteria in OTU tables for each dataset are represented as bar graphs. Data were analyzed by ANOVA followed by Tukey’s post hoc test (* P

    Techniques Used: Generated, Sequencing

    Taxonomy profiles of the Illumina MiSeq datasets. The proportion of assigned sequences ( a ) and relative abundance of the assigned sequences ( b ) from the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were determined by assigning sequences to the GG 16 S rRNA gene sequence database, and are represented at the family, genus, and species levels, respectively. Data were analyzed by ANOVA followed by Tukey’s post-hoc test (* P
    Figure Legend Snippet: Taxonomy profiles of the Illumina MiSeq datasets. The proportion of assigned sequences ( a ) and relative abundance of the assigned sequences ( b ) from the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were determined by assigning sequences to the GG 16 S rRNA gene sequence database, and are represented at the family, genus, and species levels, respectively. Data were analyzed by ANOVA followed by Tukey’s post-hoc test (* P

    Techniques Used: Sequencing

    Profile of insertion and deletion errors within each platform-generated dataset. Plots of insertion and deletion abundance for ( a ) the GG 16 S rRNA gene database (self-comparison as a control) and the ( b ) GS FLX+, ( c ) Illumina MiSeq V1–3, ( d ) MiSeq V3–4, ( e ) MiSeq V4, and ( f ) PacBio datasets. The abundance of insertions (and deletions) was normalized against sequence length.
    Figure Legend Snippet: Profile of insertion and deletion errors within each platform-generated dataset. Plots of insertion and deletion abundance for ( a ) the GG 16 S rRNA gene database (self-comparison as a control) and the ( b ) GS FLX+, ( c ) Illumina MiSeq V1–3, ( d ) MiSeq V3–4, ( e ) MiSeq V4, and ( f ) PacBio datasets. The abundance of insertions (and deletions) was normalized against sequence length.

    Techniques Used: Generated, Sequencing

    Abundance patterns of bacterial taxa in Illumina MiSeq datasets. ( a ) The abundance patterns of bacterial taxa in the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were analyzed according to linear discriminant analysis effect size (LEfSe). ( b ) The relative abundance of the families Ruminococcaceae and RF39 , and the genera Sphingomonas , Haemophilus , Methanobrevibacter , and Citrobacter in OTU tables for each dataset are represented as bar graphs. Data were analyzed by ANOVA, followed by Tukey’s post-hoc test (* P
    Figure Legend Snippet: Abundance patterns of bacterial taxa in Illumina MiSeq datasets. ( a ) The abundance patterns of bacterial taxa in the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were analyzed according to linear discriminant analysis effect size (LEfSe). ( b ) The relative abundance of the families Ruminococcaceae and RF39 , and the genera Sphingomonas , Haemophilus , Methanobrevibacter , and Citrobacter in OTU tables for each dataset are represented as bar graphs. Data were analyzed by ANOVA, followed by Tukey’s post-hoc test (* P

    Techniques Used:

    Comparative analysis of human fecal bacterial NGS datasets. Fecal samples collected from 19 human subjects were sequenced using the indicated platforms: GS FLX+ (V1–4, red), Illumina MiSeq (V1–3, light blue; V3–4, blue; V4, dark blue), and PacBio CCS (V1–9, green). Whole-genome shotgun sequences generated by Illumina HiSeq (Shotgun 16 S, orange) were included as a reference for community structure without amplification bias. ( a ) The sequence data were clustered using a UPGMA dendrogram based on the Bray-Curtis dissimilarity matrix, and samples from the same individual are shown in the same color. The relative abundances of bacterial taxa are displayed as a heatmap over 27 families ( > 1% relative abundance). ( b ) The sequence data were clustered by principal component analysis.
    Figure Legend Snippet: Comparative analysis of human fecal bacterial NGS datasets. Fecal samples collected from 19 human subjects were sequenced using the indicated platforms: GS FLX+ (V1–4, red), Illumina MiSeq (V1–3, light blue; V3–4, blue; V4, dark blue), and PacBio CCS (V1–9, green). Whole-genome shotgun sequences generated by Illumina HiSeq (Shotgun 16 S, orange) were included as a reference for community structure without amplification bias. ( a ) The sequence data were clustered using a UPGMA dendrogram based on the Bray-Curtis dissimilarity matrix, and samples from the same individual are shown in the same color. The relative abundances of bacterial taxa are displayed as a heatmap over 27 families ( > 1% relative abundance). ( b ) The sequence data were clustered by principal component analysis.

    Techniques Used: Next-Generation Sequencing, Generated, Amplification, Sequencing

    4) Product Images from "Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies"

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

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-23296-4

    Donor specificity is maintained independent of experimental pipeline. ( a ) PCA bi-plots of clr transformed data on Illumina MiSeq and Ion Torrent PGM sequencing platforms. ( b ) Relative abundance profiles of individual subjects on each platform for top 20 families. ( c ) Relative abundances per platform represented as mean ± SD, with R 2 values displayed from linear model fitted to log10 values.
    Figure Legend Snippet: Donor specificity is maintained independent of experimental pipeline. ( a ) PCA bi-plots of clr transformed data on Illumina MiSeq and Ion Torrent PGM sequencing platforms. ( b ) Relative abundance profiles of individual subjects on each platform for top 20 families. ( c ) Relative abundances per platform represented as mean ± SD, with R 2 values displayed from linear model fitted to log10 values.

    Techniques Used: Transformation Assay, 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.
    Figure Legend 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.

    Techniques Used: Sequencing

    5) Product Images from "A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery"

    Article Title: A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery

    Journal: Virology

    doi: 10.1016/j.virol.2018.12.020

    Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBSplit to the appropriate reference sequence, 16S bacterial rRNA (A), 23S bacterial rRNA (B), Elizabethkingia anophelis transcriptome (C and D) and the NCBI bacterial genome database (E). The reads called for each gene was determined using BBMap with output flag rpkm (D). All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.
    Figure Legend Snippet: Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBSplit to the appropriate reference sequence, 16S bacterial rRNA (A), 23S bacterial rRNA (B), Elizabethkingia anophelis transcriptome (C and D) and the NCBI bacterial genome database (E). The reads called for each gene was determined using BBMap with output flag rpkm (D). All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.

    Techniques Used: Purification, Sequencing

    Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBMap or BBSplit to the appropriate reference sequence, An. gambiae transcriptome (A and B), West Nile virus (C) or Bolahun virus (D). The reads called for each gene was determined using BBMap with output flag rpkm (B). Variants detected in Bolahun virus were called using LoFreq (F). Only variants present at greater than 5% were used for analysis. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.
    Figure Legend Snippet: Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBMap or BBSplit to the appropriate reference sequence, An. gambiae transcriptome (A and B), West Nile virus (C) or Bolahun virus (D). The reads called for each gene was determined using BBMap with output flag rpkm (B). Variants detected in Bolahun virus were called using LoFreq (F). Only variants present at greater than 5% were used for analysis. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.

    Techniques Used: Purification, Sequencing

    Reverse Transcriptase mediated ribosomal RNA (rRNA) depletion increases target-specific coverage while reducing the number of rRNA reads in next-generation sequencing. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNase H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using BBSplit to the appropriate reference sequence, unique reads after duplicate removal (A), 18S rRNA (B), 28S rRNA (C) and mitochondrial 16S rRNA (D). Reads for 18S (E) and 28S (F) rRNA were then normalized to host gene AGAP001826-RA and then compared. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.
    Figure Legend Snippet: Reverse Transcriptase mediated ribosomal RNA (rRNA) depletion increases target-specific coverage while reducing the number of rRNA reads in next-generation sequencing. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNase H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using BBSplit to the appropriate reference sequence, unique reads after duplicate removal (A), 18S rRNA (B), 28S rRNA (C) and mitochondrial 16S rRNA (D). Reads for 18S (E) and 28S (F) rRNA were then normalized to host gene AGAP001826-RA and then compared. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.

    Techniques Used: Next-Generation Sequencing, Purification, Sequencing

    6) Product Images from "TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration"

    Article Title: TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-36669-6

    Number of variable sites in SiHa replicates. SiHa-1 (red dots) and SiHa-2 (blue dots) served as technical replicates to assess the variant calling performance. In SiHa libraries, sequenced on MiSeq and HiSeq 2500 platforms, increasing number of variable sites were detected with higher mean coverage.
    Figure Legend Snippet: Number of variable sites in SiHa replicates. SiHa-1 (red dots) and SiHa-2 (blue dots) served as technical replicates to assess the variant calling performance. In SiHa libraries, sequenced on MiSeq and HiSeq 2500 platforms, increasing number of variable sites were detected with higher mean coverage.

    Techniques Used: Variant Assay

    7) Product Images from "The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces"

    Article Title: The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces

    Journal: Scientific Data

    doi: 10.1038/sdata.2018.68

    Relationship between sequence read length and assignment to database. ( a and b ) Sequences ( n =10,000) covering the V1–4 (red), V1–3 (light blue), V3–4 (blue), V4 (dark blue), and V1–9 (green) regions of the 16 S rRNA gene were extracted in silico from the GG 16 S rRNA gene database. ( a ) Pairwise similarities between targeted regions are represented as similarity distributions (lower left), similarity histograms (diagonal), and correlation coefficient values (upper right). ( b ) Accuracy of phylogenetic reconstruction per targeted region. Precision (x-axis) and recall (y-axis) were calculated based on 100 randomly chosen bootstrap replications. ( c ) Distribution of sequence (30,000 sub-sampled) similarities, including and excluding indel errors, between data generated by GS FLX+, Illumina MiSeq, and PacBio, and data from publically available PacBio sequences.
    Figure Legend Snippet: Relationship between sequence read length and assignment to database. ( a and b ) Sequences ( n =10,000) covering the V1–4 (red), V1–3 (light blue), V3–4 (blue), V4 (dark blue), and V1–9 (green) regions of the 16 S rRNA gene were extracted in silico from the GG 16 S rRNA gene database. ( a ) Pairwise similarities between targeted regions are represented as similarity distributions (lower left), similarity histograms (diagonal), and correlation coefficient values (upper right). ( b ) Accuracy of phylogenetic reconstruction per targeted region. Precision (x-axis) and recall (y-axis) were calculated based on 100 randomly chosen bootstrap replications. ( c ) Distribution of sequence (30,000 sub-sampled) similarities, including and excluding indel errors, between data generated by GS FLX+, Illumina MiSeq, and PacBio, and data from publically available PacBio sequences.

    Techniques Used: Sequencing, In Silico, Generated

    Taxonomy profiles of the Illumina MiSeq datasets. The proportion of assigned sequences ( a ) and relative abundance of the assigned sequences ( b ) from the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were determined by assigning sequences to the GG 16 S rRNA gene sequence database, and are represented at the fami ly, genus, and species levels, respectively. Data were analyzed by ANOVA followed by Tukey’s post-hoc test (* P
    Figure Legend Snippet: Taxonomy profiles of the Illumina MiSeq datasets. The proportion of assigned sequences ( a ) and relative abundance of the assigned sequences ( b ) from the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were determined by assigning sequences to the GG 16 S rRNA gene sequence database, and are represented at the fami ly, genus, and species levels, respectively. Data were analyzed by ANOVA followed by Tukey’s post-hoc test (* P

    Techniques Used: Sequencing

    Abundance patterns of bacterial taxa in Illumina MiSeq datasets. ( a ) The abundance patterns of bacterial taxa in the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were analyzed according to linear discriminant analysis effect size (LEfSe). ( b ) The relative abundance of the families Ruminococcaceae and RF39 , and the genera Sphingomonas , Haemophilus , Methanobrevibacter , and Citrobacter in OTU tables for each dataset are represented as bar graphs. Data were analyzed by ANOVA, followed by Tukey’s post-hoc test (* P
    Figure Legend Snippet: Abundance patterns of bacterial taxa in Illumina MiSeq datasets. ( a ) The abundance patterns of bacterial taxa in the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were analyzed according to linear discriminant analysis effect size (LEfSe). ( b ) The relative abundance of the families Ruminococcaceae and RF39 , and the genera Sphingomonas , Haemophilus , Methanobrevibacter , and Citrobacter in OTU tables for each dataset are represented as bar graphs. Data were analyzed by ANOVA, followed by Tukey’s post-hoc test (* P

    Techniques Used:

    8) Product Images from "Evidence for positive selection of hepatitis A virus antigenic variants in vaccinated men-having-sex-with men patients: Implications for immunization policies"

    Article Title: Evidence for positive selection of hepatitis A virus antigenic variants in vaccinated men-having-sex-with men patients: Implications for immunization policies

    Journal: EBioMedicine

    doi: 10.1016/j.ebiom.2018.11.023

    Phylogenetic analysis of HAV strains isolated from patients of the men-having-sex-with-men (MSM) 2016–2018 outbreak from Barcelona. (a) Phylogenetic tree based on a 255-bp fragment (spanning positions 2958–3230) from the VP1/2A protein. (b) Phylogenetic tree based on a sequence of 91-amino acids (spanning positions 251–300 from VP1 and 1–41 from 2A). (c) Phylogenetic tree based on a 1004-bp fragment (spanning positions 2208–3212) including the complete VP1 sequence and a short fragment of 2A. (d) Phylogenetic tree based on a sequence of 334-amino acids (spanning positions 1–300 from VP1 and 1–35 from 2A). Nucleotide dendrograms were constructed using the neighbour-joining method with distance calculation by the Kimura-2-parameter, and performing a bootstrap of 1000 replicates. Amino acid dendograms were constructed using the Neighbour-Joining method with distance calculation using the Poisson correction method. Samples from vaccinated individuals ( n = 5) are underlined, samples from HIV-infected patients ( n = 6) are indicated with the “†” symbol. Samples further analysed by MiSeq Illumina ( n = 13) are indicated with “*”. The three main circulating strains in Europe related to this outbreak, VRD_521_20166, RIVM-HAV16-0907, and V16-258018A are included, and labelled in bold, as well as five representative samples from a previous MSM outbreak in Barcelona from 2008 to 09 (MSM08-09). Additionally, eleven reference strains representative of all subgenotypes (subgenotype IA: AB020565, EU13137, X83302; subgenotype IB: M14707, M59808, DQ646426, subgenotype IC: HQ401240; subgenotype IIA: AY644676; subgenotype IIB: AY644670; subgenotype IIIA: AB279733; subgenotype IIIB: AB425339), including the HM175 strain used in the TWINRIX vaccine (subgenotype IB), were also added. All tested samples were obtained in the period 2016–2017.
    Figure Legend Snippet: Phylogenetic analysis of HAV strains isolated from patients of the men-having-sex-with-men (MSM) 2016–2018 outbreak from Barcelona. (a) Phylogenetic tree based on a 255-bp fragment (spanning positions 2958–3230) from the VP1/2A protein. (b) Phylogenetic tree based on a sequence of 91-amino acids (spanning positions 251–300 from VP1 and 1–41 from 2A). (c) Phylogenetic tree based on a 1004-bp fragment (spanning positions 2208–3212) including the complete VP1 sequence and a short fragment of 2A. (d) Phylogenetic tree based on a sequence of 334-amino acids (spanning positions 1–300 from VP1 and 1–35 from 2A). Nucleotide dendrograms were constructed using the neighbour-joining method with distance calculation by the Kimura-2-parameter, and performing a bootstrap of 1000 replicates. Amino acid dendograms were constructed using the Neighbour-Joining method with distance calculation using the Poisson correction method. Samples from vaccinated individuals ( n = 5) are underlined, samples from HIV-infected patients ( n = 6) are indicated with the “†” symbol. Samples further analysed by MiSeq Illumina ( n = 13) are indicated with “*”. The three main circulating strains in Europe related to this outbreak, VRD_521_20166, RIVM-HAV16-0907, and V16-258018A are included, and labelled in bold, as well as five representative samples from a previous MSM outbreak in Barcelona from 2008 to 09 (MSM08-09). Additionally, eleven reference strains representative of all subgenotypes (subgenotype IA: AB020565, EU13137, X83302; subgenotype IB: M14707, M59808, DQ646426, subgenotype IC: HQ401240; subgenotype IIA: AY644676; subgenotype IIB: AY644670; subgenotype IIIA: AB279733; subgenotype IIIB: AB425339), including the HM175 strain used in the TWINRIX vaccine (subgenotype IB), were also added. All tested samples were obtained in the period 2016–2017.

    Techniques Used: Isolation, Sequencing, Construct, Infection, IA

    9) Product Images from "Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP – A Bioinformatics Pipeline for Analyzing nifH Amplicon Data"

    Article Title: Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP – A Bioinformatics Pipeline for Analyzing nifH Amplicon Data

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2018.00703

    Schematic overview of NifMAP – Nif H M iSeq Illumina Amplicon A nalysis P ipeline. Pipeline begins with raw MiSeq reads from desired sequencing facility (depicted in gray). Steps shaded in blue represent standard processing steps, while steps shaded in green represent steps specific for processing nifH sequences, introduced in this work.
    Figure Legend Snippet: Schematic overview of NifMAP – Nif H M iSeq Illumina Amplicon A nalysis P ipeline. Pipeline begins with raw MiSeq reads from desired sequencing facility (depicted in gray). Steps shaded in blue represent standard processing steps, while steps shaded in green represent steps specific for processing nifH sequences, introduced in this work.

    Techniques Used: Amplification, Sequencing

    10) Product Images from "Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer"

    Article Title: Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-35750-4

    Phylogenetic tree of the genome sequences of the 2016 WHO Neisseria gonorrhoeae reference strains (n = 14) 40 , 41 and clinical gonococcal isolates (n = 14) sequenced with Illumina MiSeq and MinION (Oxford Nanopore Technologies (ONT)). The tree uses the genome of the N. gonorrhoeae reference strain FA1090 as reference (shown with black bar). The platform used, number of reads, average read length, and number of single nucleotide polymorphisms (SNPs) are displayed as colored bars next to each node in the tree. The numbers inside the SNP-bars is the pairwise distance between the Illumina and 2D ONT sequences.
    Figure Legend Snippet: Phylogenetic tree of the genome sequences of the 2016 WHO Neisseria gonorrhoeae reference strains (n = 14) 40 , 41 and clinical gonococcal isolates (n = 14) sequenced with Illumina MiSeq and MinION (Oxford Nanopore Technologies (ONT)). The tree uses the genome of the N. gonorrhoeae reference strain FA1090 as reference (shown with black bar). The platform used, number of reads, average read length, and number of single nucleotide polymorphisms (SNPs) are displayed as colored bars next to each node in the tree. The numbers inside the SNP-bars is the pairwise distance between the Illumina and 2D ONT sequences.

    Techniques Used:

    11) Product Images from "Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer"

    Article Title: Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-35750-4

    Phylogenetic tree of the genome sequences of the 2016 WHO Neisseria gonorrhoeae and clinical gonococcal isolates (n = 14) sequenced with Illumina MiSeq and MinION (Oxford Nanopore Technologies (ONT)). The tree uses the genome of the N. gonorrhoeae reference strain FA1090 as reference (shown with black bar). The platform used, number of reads, average read length, and number of single nucleotide polymorphisms (SNPs) are displayed as colored bars next to each node in the tree. The numbers inside the SNP-bars is the pairwise distance between the Illumina and 2D ONT sequences.
    Figure Legend Snippet: Phylogenetic tree of the genome sequences of the 2016 WHO Neisseria gonorrhoeae and clinical gonococcal isolates (n = 14) sequenced with Illumina MiSeq and MinION (Oxford Nanopore Technologies (ONT)). The tree uses the genome of the N. gonorrhoeae reference strain FA1090 as reference (shown with black bar). The platform used, number of reads, average read length, and number of single nucleotide polymorphisms (SNPs) are displayed as colored bars next to each node in the tree. The numbers inside the SNP-bars is the pairwise distance between the Illumina and 2D ONT sequences.

    Techniques Used:

    12) Product Images from "Miniaturisation of high-throughput plasmid DNA library preparation for next-generation sequencing using multifactorial optimisation"

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

    Journal: Synthetic and Systems Biotechnology

    doi: 10.1016/j.synbio.2019.01.002

    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.
    Figure Legend 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.

    Techniques Used: 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.
    Figure Legend 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.

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

    13) Product Images from "Deconvolution of nucleic-acid length distributions: a gel electrophoresis analysis tool and applications"

    Article Title: Deconvolution of nucleic-acid length distributions: a gel electrophoresis analysis tool and applications

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkz534

    Fragment-library size distributions obtained from bioinformatic analysis of MiSeq sequencing output. A tagmented sample of phage λ genomic DNA was subjected to 8, 14 and 20 cycles of PCR amplification, respectively. The fragment counts in each bin are normalized with respect to the maximum value in each distribution.
    Figure Legend Snippet: Fragment-library size distributions obtained from bioinformatic analysis of MiSeq sequencing output. A tagmented sample of phage λ genomic DNA was subjected to 8, 14 and 20 cycles of PCR amplification, respectively. The fragment counts in each bin are normalized with respect to the maximum value in each distribution.

    Techniques Used: Sequencing, Polymerase Chain Reaction, Amplification

    14) Product Images from "The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces"

    Article Title: The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces

    Journal: Scientific Data

    doi: 10.1038/sdata.2018.68

    Relationship between sequence read length and assignment to database. ( a and b ) Sequences ( n =10,000) covering the V1–4 (red), V1–3 (light blue), V3–4 (blue), V4 (dark blue), and V1–9 (green) regions of the 16 S rRNA gene were extracted in silico from the GG 16 S rRNA gene database. ( a ) Pairwise similarities between targeted regions are represented as similarity distributions (lower left), similarity histograms (diagonal), and correlation coefficient values (upper right). ( b ) Accuracy of phylogenetic reconstruction per targeted region. Precision (x-axis) and recall (y-axis) were calculated based on 100 randomly chosen bootstrap replications. ( c ) Distribution of sequence (30,000 sub-sampled) similarities, including and excluding indel errors, between data generated by GS FLX+, Illumina MiSeq, and PacBio, and data from publically available PacBio sequences.
    Figure Legend Snippet: Relationship between sequence read length and assignment to database. ( a and b ) Sequences ( n =10,000) covering the V1–4 (red), V1–3 (light blue), V3–4 (blue), V4 (dark blue), and V1–9 (green) regions of the 16 S rRNA gene were extracted in silico from the GG 16 S rRNA gene database. ( a ) Pairwise similarities between targeted regions are represented as similarity distributions (lower left), similarity histograms (diagonal), and correlation coefficient values (upper right). ( b ) Accuracy of phylogenetic reconstruction per targeted region. Precision (x-axis) and recall (y-axis) were calculated based on 100 randomly chosen bootstrap replications. ( c ) Distribution of sequence (30,000 sub-sampled) similarities, including and excluding indel errors, between data generated by GS FLX+, Illumina MiSeq, and PacBio, and data from publically available PacBio sequences.

    Techniques Used: Sequencing, In Silico, Generated

    Taxonomy profiles in each platform-generated datasets. ( a ) The proportion of assigned sequences from the GS FLX+ ( n =169, red), MiSeq V4 ( n =169, blue), and PacBio ( n =29, green) datasets was determined by assigning the sequences to the GG 16 S rRNA gene sequence database, and are represented at the family, genus, and species levels. ( b ) The abundance patterns of bacterial taxa in each dataset were analyzed using the linear discriminant analysis effect size (LEfSe) circular cladogram. The discriminant taxa for the GS FLX+, MiSeq V4, and PacBio datasets are shown in red, blue, and green, respectively. ( c ) Relative abundances of the phylum Bacteroidetes , Actinobacteria and Proteobacteria in OTU tables for each dataset are represented as bar graphs. Data were analyzed by ANOVA followed by Tukey’s post hoc test (* P
    Figure Legend Snippet: Taxonomy profiles in each platform-generated datasets. ( a ) The proportion of assigned sequences from the GS FLX+ ( n =169, red), MiSeq V4 ( n =169, blue), and PacBio ( n =29, green) datasets was determined by assigning the sequences to the GG 16 S rRNA gene sequence database, and are represented at the family, genus, and species levels. ( b ) The abundance patterns of bacterial taxa in each dataset were analyzed using the linear discriminant analysis effect size (LEfSe) circular cladogram. The discriminant taxa for the GS FLX+, MiSeq V4, and PacBio datasets are shown in red, blue, and green, respectively. ( c ) Relative abundances of the phylum Bacteroidetes , Actinobacteria and Proteobacteria in OTU tables for each dataset are represented as bar graphs. Data were analyzed by ANOVA followed by Tukey’s post hoc test (* P

    Techniques Used: Generated, Sequencing

    Taxonomy profiles of the Illumina MiSeq datasets. The proportion of assigned sequences ( a ) and relative abundance of the assigned sequences ( b ) from the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were determined by assigning sequences to the GG 16 S rRNA gene sequence database, and are represented at the family, genus, and species levels, respectively. Data were analyzed by ANOVA followed by Tukey’s post-hoc test (* P
    Figure Legend Snippet: Taxonomy profiles of the Illumina MiSeq datasets. The proportion of assigned sequences ( a ) and relative abundance of the assigned sequences ( b ) from the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were determined by assigning sequences to the GG 16 S rRNA gene sequence database, and are represented at the family, genus, and species levels, respectively. Data were analyzed by ANOVA followed by Tukey’s post-hoc test (* P

    Techniques Used: Sequencing

    Profile of insertion and deletion errors within each platform-generated dataset. Plots of insertion and deletion abundance for ( a ) the GG 16 S rRNA gene database (self-comparison as a control) and the ( b ) GS FLX+, ( c ) Illumina MiSeq V1–3, ( d ) MiSeq V3–4, ( e ) MiSeq V4, and ( f ) PacBio datasets. The abundance of insertions (and deletions) was normalized against sequence length.
    Figure Legend Snippet: Profile of insertion and deletion errors within each platform-generated dataset. Plots of insertion and deletion abundance for ( a ) the GG 16 S rRNA gene database (self-comparison as a control) and the ( b ) GS FLX+, ( c ) Illumina MiSeq V1–3, ( d ) MiSeq V3–4, ( e ) MiSeq V4, and ( f ) PacBio datasets. The abundance of insertions (and deletions) was normalized against sequence length.

    Techniques Used: Generated, Sequencing

    Abundance patterns of bacterial taxa in Illumina MiSeq datasets. ( a ) The abundance patterns of bacterial taxa in the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were analyzed according to linear discriminant analysis effect size (LEfSe). ( b ) The relative abundance of the families Ruminococcaceae and RF39 , and the genera Sphingomonas , Haemophilus , Methanobrevibacter , and Citrobacter in OTU tables for each dataset are represented as bar graphs. Data were analyzed by ANOVA, followed by Tukey’s post-hoc test (* P
    Figure Legend Snippet: Abundance patterns of bacterial taxa in Illumina MiSeq datasets. ( a ) The abundance patterns of bacterial taxa in the MiSeq V1–3 ( n =165, light blue), V3–4 ( n =165, blue), and V4 ( n =165, dark blue) datasets were analyzed according to linear discriminant analysis effect size (LEfSe). ( b ) The relative abundance of the families Ruminococcaceae and RF39 , and the genera Sphingomonas , Haemophilus , Methanobrevibacter , and Citrobacter in OTU tables for each dataset are represented as bar graphs. Data were analyzed by ANOVA, followed by Tukey’s post-hoc test (* P

    Techniques Used:

    Comparative analysis of human fecal bacterial NGS datasets. Fecal samples collected from 19 human subjects were sequenced using the indicated platforms: GS FLX+ (V1–4, red), Illumina MiSeq (V1–3, light blue; V3–4, blue; V4, dark blue), and PacBio CCS (V1–9, green). Whole-genome shotgun sequences generated by Illumina HiSeq (Shotgun 16 S, orange) were included as a reference for community structure without amplification bias. ( a ) The sequence data were clustered using a UPGMA dendrogram based on the Bray-Curtis dissimilarity matrix, and samples from the same individual are shown in the same color. The relative abundances of bacterial taxa are displayed as a heatmap over 27 families ( > 1% relative abundance). ( b ) The sequence data were clustered by principal component analysis.
    Figure Legend Snippet: Comparative analysis of human fecal bacterial NGS datasets. Fecal samples collected from 19 human subjects were sequenced using the indicated platforms: GS FLX+ (V1–4, red), Illumina MiSeq (V1–3, light blue; V3–4, blue; V4, dark blue), and PacBio CCS (V1–9, green). Whole-genome shotgun sequences generated by Illumina HiSeq (Shotgun 16 S, orange) were included as a reference for community structure without amplification bias. ( a ) The sequence data were clustered using a UPGMA dendrogram based on the Bray-Curtis dissimilarity matrix, and samples from the same individual are shown in the same color. The relative abundances of bacterial taxa are displayed as a heatmap over 27 families ( > 1% relative abundance). ( b ) The sequence data were clustered by principal component analysis.

    Techniques Used: Next-Generation Sequencing, Generated, Amplification, Sequencing

    15) Product Images from "Intra-host sequence variability in human papillomavirus"

    Article Title: Intra-host sequence variability in human papillomavirus

    Journal: Papillomavirus Research

    doi: 10.1016/j.pvr.2018.04.006

    Summary of phylogenetic tree construction from 144 women who each provided duplicate samples (anal + vaginal swabs). The L1 region of HPV was sequenced using next generation sequencing on the Illumina MiSeq platform. The sequence pairs generated were filtered, clustered and aligned to produce 35 phylogenetic trees. HPV 16, 18 and 52 were further analysed for in-depth statistical description of the distribution of clades by site of HPV infection, cervical cytology result and HIV statuses of the women.
    Figure Legend Snippet: Summary of phylogenetic tree construction from 144 women who each provided duplicate samples (anal + vaginal swabs). The L1 region of HPV was sequenced using next generation sequencing on the Illumina MiSeq platform. The sequence pairs generated were filtered, clustered and aligned to produce 35 phylogenetic trees. HPV 16, 18 and 52 were further analysed for in-depth statistical description of the distribution of clades by site of HPV infection, cervical cytology result and HIV statuses of the women.

    Techniques Used: Next-Generation Sequencing, Sequencing, Generated, Infection

    16) Product Images from "Evidence for positive selection of hepatitis A virus antigenic variants in vaccinated men-having-sex-with men patients: Implications for immunization policies"

    Article Title: Evidence for positive selection of hepatitis A virus antigenic variants in vaccinated men-having-sex-with men patients: Implications for immunization policies

    Journal: EBioMedicine

    doi: 10.1016/j.ebiom.2018.11.023

    Phylogenetic analysis of HAV strains isolated from patients of the men-having-sex-with-men (MSM) 2016–2018 outbreak from Barcelona. (a) Phylogenetic tree based on a 255-bp fragment (spanning positions 2958–3230) from the VP1/2A protein. (b) Phylogenetic tree based on a sequence of 91-amino acids (spanning positions 251–300 from VP1 and 1–41 from 2A). (c) Phylogenetic tree based on a 1004-bp fragment (spanning positions 2208–3212) including the complete VP1 sequence and a short fragment of 2A. (d) Phylogenetic tree based on a sequence of 334-amino acids (spanning positions 1–300 from VP1 and 1–35 from 2A). Nucleotide dendrograms were constructed using the neighbour-joining method with distance calculation by the Kimura-2-parameter, and performing a bootstrap of 1000 replicates. Amino acid dendograms were constructed using the Neighbour-Joining method with distance calculation using the Poisson correction method. Samples from vaccinated individuals ( n = 5) are underlined, samples from HIV-infected patients ( n = 6) are indicated with the “†” symbol. Samples further analysed by MiSeq Illumina ( n = 13) are indicated with “*”. The three main circulating strains in Europe related to this outbreak, VRD_521_20166, RIVM-HAV16-0907, and V16-258018A are included, and labelled in bold, as well as five representative samples from a previous MSM outbreak in Barcelona from 2008 to 09 (MSM08-09). Additionally, eleven reference strains representative of all subgenotypes (subgenotype IA: AB020565, EU13137, X83302; subgenotype IB: M14707, M59808, DQ646426, subgenotype IC: HQ401240; subgenotype IIA: AY644676; subgenotype IIB: AY644670; subgenotype IIIA: AB279733; subgenotype IIIB: AB425339), including the HM175 strain used in the TWINRIX vaccine (subgenotype IB), were also added. All tested samples were obtained in the period 2016–2017.
    Figure Legend Snippet: Phylogenetic analysis of HAV strains isolated from patients of the men-having-sex-with-men (MSM) 2016–2018 outbreak from Barcelona. (a) Phylogenetic tree based on a 255-bp fragment (spanning positions 2958–3230) from the VP1/2A protein. (b) Phylogenetic tree based on a sequence of 91-amino acids (spanning positions 251–300 from VP1 and 1–41 from 2A). (c) Phylogenetic tree based on a 1004-bp fragment (spanning positions 2208–3212) including the complete VP1 sequence and a short fragment of 2A. (d) Phylogenetic tree based on a sequence of 334-amino acids (spanning positions 1–300 from VP1 and 1–35 from 2A). Nucleotide dendrograms were constructed using the neighbour-joining method with distance calculation by the Kimura-2-parameter, and performing a bootstrap of 1000 replicates. Amino acid dendograms were constructed using the Neighbour-Joining method with distance calculation using the Poisson correction method. Samples from vaccinated individuals ( n = 5) are underlined, samples from HIV-infected patients ( n = 6) are indicated with the “†” symbol. Samples further analysed by MiSeq Illumina ( n = 13) are indicated with “*”. The three main circulating strains in Europe related to this outbreak, VRD_521_20166, RIVM-HAV16-0907, and V16-258018A are included, and labelled in bold, as well as five representative samples from a previous MSM outbreak in Barcelona from 2008 to 09 (MSM08-09). Additionally, eleven reference strains representative of all subgenotypes (subgenotype IA: AB020565, EU13137, X83302; subgenotype IB: M14707, M59808, DQ646426, subgenotype IC: HQ401240; subgenotype IIA: AY644676; subgenotype IIB: AY644670; subgenotype IIIA: AB279733; subgenotype IIIB: AB425339), including the HM175 strain used in the TWINRIX vaccine (subgenotype IB), were also added. All tested samples were obtained in the period 2016–2017.

    Techniques Used: Isolation, Sequencing, Construct, Infection, IA

    17) Product Images from "Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis"

    Article Title: Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis

    Journal: The Journal of Molecular Diagnostics : JMD

    doi: 10.1016/j.jmoldx.2015.11.005

    Assay workflow for comprehensive CFTR sequencing using blood spots from newborns. Listed are the times for individual steps, when 96 specimens are multiplexed. Computation time for copy number variant (CNV) analysis can vary based on server cluster specifications, and therefore an estimated range is provided based on whether each sample is analyzed sequentially or in parallel ( asterisk ). DBS, dried blood spot; mPCR, multiplex PCR; MiSeq, MiSeq platform (Illumina, San Diego, CA); QC, quality control.
    Figure Legend Snippet: Assay workflow for comprehensive CFTR sequencing using blood spots from newborns. Listed are the times for individual steps, when 96 specimens are multiplexed. Computation time for copy number variant (CNV) analysis can vary based on server cluster specifications, and therefore an estimated range is provided based on whether each sample is analyzed sequentially or in parallel ( asterisk ). DBS, dried blood spot; mPCR, multiplex PCR; MiSeq, MiSeq platform (Illumina, San Diego, CA); QC, quality control.

    Techniques Used: Sequencing, Variant Assay, Multiplex Assay, Polymerase Chain Reaction

    18) Product Images from "A probiotic modulates the microbiome and immunity in multiple sclerosis"

    Article Title: A probiotic modulates the microbiome and immunity in multiple sclerosis

    Journal: Annals of neurology

    doi: 10.1002/ana.25244

    Study design flowchart Blood and fecal samples were collected from healthy subjects (n=13) and multiple sclerosis (MS) patients (n=9) prior to (baseline), at discontinuation of probiotic LBS (2-month visit) and 3 months thereafter (5-month visit). Bacteria DNA was extracted from feces samples obtained at all 3 time points and 16S rRNA sequencing was performed using Illumina MiSeq.16S data was used to obtain predicted metagenomics by PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States). Feces samples were also used for stool metabolomics profiling at all 3 time points. Immune cells profiling was performed in healthy subjects and MS patients at all 3 time points by flow cytometry. Gene expression profiling was performed on peripheral monocytes and CD4 T cells from healthy controls and MS patients using a Nanostring immunology panel array and high-throughput eukaryotic digital gene expression RNA-Seq (RNA-DGE) respectively.
    Figure Legend Snippet: Study design flowchart Blood and fecal samples were collected from healthy subjects (n=13) and multiple sclerosis (MS) patients (n=9) prior to (baseline), at discontinuation of probiotic LBS (2-month visit) and 3 months thereafter (5-month visit). Bacteria DNA was extracted from feces samples obtained at all 3 time points and 16S rRNA sequencing was performed using Illumina MiSeq.16S data was used to obtain predicted metagenomics by PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States). Feces samples were also used for stool metabolomics profiling at all 3 time points. Immune cells profiling was performed in healthy subjects and MS patients at all 3 time points by flow cytometry. Gene expression profiling was performed on peripheral monocytes and CD4 T cells from healthy controls and MS patients using a Nanostring immunology panel array and high-throughput eukaryotic digital gene expression RNA-Seq (RNA-DGE) respectively.

    Techniques Used: Mass Spectrometry, Sequencing, Flow Cytometry, Cytometry, Expressing, High Throughput Screening Assay, RNA Sequencing Assay

    19) Product Images from "Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies"

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

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-23296-4

    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.
    Figure Legend 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.

    Techniques Used: Sequencing

    20) Product Images from "Mutant TRP53 exerts a target gene-selective dominant-negative effect to drive tumor development"

    Article Title: Mutant TRP53 exerts a target gene-selective dominant-negative effect to drive tumor development

    Journal: Genes & Development

    doi: 10.1101/gad.314286.118

    Overexpression of mutant TRP53 proteins accelerates lymphoma development in an Eμ-Myc;Trp53 +/+ background and relieves selective pressure for mutation of endogenous Trp53 genes. ( A ) Kaplan-Meier survival curves for mice reconstituted with Eμ-Myc;Trp53 +/+ HSPCs comparing empty vector control (pMIG), CRISPR/Cas9 Trp53 knockout , and each mutant TRP53 protein (V170M, I192S, G280, R246Q, and R270H). P -values were determined by log rank (Mantel-Cox) test. ( B ) Selected TRP53 protein immunohistochemistry in lymphomas from the Eμ-Myc hematopoietic reconstitution experiments (mice #88 and #541 plus control mouse #53). ( C ) Endogenous Trp53 allele copy number in lymphomas from the Eμ-Myc hematopoietic reconstitution experiments as determined by genomic DNA quantitative PCR (pMIG/control: #53; V170M: #55, #66, and #541; G280: #68 and #81; I192S: #72 and #546; R246Q: #97 and #98; R270H: #80, #543, and #544). Primary cells from Trp53 −/− and Trp53 +/− mice were used as controls. Data from MiSeq analysis throughout the coding region of the DNA-binding domain (exons 4–10) are indicated. (wt) Wild-type sequence. Data represent mean ± SEM. (*) P
    Figure Legend Snippet: Overexpression of mutant TRP53 proteins accelerates lymphoma development in an Eμ-Myc;Trp53 +/+ background and relieves selective pressure for mutation of endogenous Trp53 genes. ( A ) Kaplan-Meier survival curves for mice reconstituted with Eμ-Myc;Trp53 +/+ HSPCs comparing empty vector control (pMIG), CRISPR/Cas9 Trp53 knockout , and each mutant TRP53 protein (V170M, I192S, G280, R246Q, and R270H). P -values were determined by log rank (Mantel-Cox) test. ( B ) Selected TRP53 protein immunohistochemistry in lymphomas from the Eμ-Myc hematopoietic reconstitution experiments (mice #88 and #541 plus control mouse #53). ( C ) Endogenous Trp53 allele copy number in lymphomas from the Eμ-Myc hematopoietic reconstitution experiments as determined by genomic DNA quantitative PCR (pMIG/control: #53; V170M: #55, #66, and #541; G280: #68 and #81; I192S: #72 and #546; R246Q: #97 and #98; R270H: #80, #543, and #544). Primary cells from Trp53 −/− and Trp53 +/− mice were used as controls. Data from MiSeq analysis throughout the coding region of the DNA-binding domain (exons 4–10) are indicated. (wt) Wild-type sequence. Data represent mean ± SEM. (*) P

    Techniques Used: Over Expression, Mutagenesis, Mouse Assay, Plasmid Preparation, CRISPR, Knock-Out, Immunohistochemistry, Real-time Polymerase Chain Reaction, Binding Assay, Sequencing

    21) Product Images from "Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution"

    Article Title: Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

    Journal: bioRxiv

    doi: 10.1101/2020.05.06.078147

    Comparison of taxonomic profiles of human gut microbiota between sequencing methodologies. Six fecal samples (F1-F6) were analyzed by sequencing the entire 16S rRNA gene using MinION™ (N_V1-V9). For comparison, the V3-V4 region was sequenced on MinION™ (N_V3-V4) or MiSeq™ platforms (I_V1-V9). Randomly sampled 20000 reads from each data set were allocated to the reference genome database of 5850 representative bacterial species. A heat map shows the relative genus abundance (%) of classified reads. The 15 most abundant taxa are shown. The Pearson correlation coefficient ( r ) between sequencing methods was computed. Asterisks indicate significant correlations at P
    Figure Legend Snippet: Comparison of taxonomic profiles of human gut microbiota between sequencing methodologies. Six fecal samples (F1-F6) were analyzed by sequencing the entire 16S rRNA gene using MinION™ (N_V1-V9). For comparison, the V3-V4 region was sequenced on MinION™ (N_V3-V4) or MiSeq™ platforms (I_V1-V9). Randomly sampled 20000 reads from each data set were allocated to the reference genome database of 5850 representative bacterial species. A heat map shows the relative genus abundance (%) of classified reads. The 15 most abundant taxa are shown. The Pearson correlation coefficient ( r ) between sequencing methods was computed. Asterisks indicate significant correlations at P

    Techniques Used: Sequencing

    Comparison of taxonomic resolution. The percentages of ambiguous reads not assigned to the species level are plotted for six fecal samples analyzed by MinION™ (N_V1-V9 and N_V3-V4) or MiSeq™ (I_V3-V4). Horizontal bars represent mean values. * P
    Figure Legend Snippet: Comparison of taxonomic resolution. The percentages of ambiguous reads not assigned to the species level are plotted for six fecal samples analyzed by MinION™ (N_V1-V9 and N_V3-V4) or MiSeq™ (I_V3-V4). Horizontal bars represent mean values. * P

    Techniques Used:

    22) Product Images from "TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration"

    Article Title: TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-36669-6

    Number of variable sites in SiHa replicates. SiHa-1 (red dots) and SiHa-2 (blue dots) served as technical replicates to assess the variant calling performance. In SiHa libraries, sequenced on MiSeq and HiSeq 2500 platforms, increasing number of variable sites were detected with higher mean coverage.
    Figure Legend Snippet: Number of variable sites in SiHa replicates. SiHa-1 (red dots) and SiHa-2 (blue dots) served as technical replicates to assess the variant calling performance. In SiHa libraries, sequenced on MiSeq and HiSeq 2500 platforms, increasing number of variable sites were detected with higher mean coverage.

    Techniques Used: Variant Assay

    23) Product Images from "A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection"

    Article Title: A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection

    Journal: BMC Genomics

    doi: 10.1186/s12864-017-3714-6

    The procedure for rotavirus capture and nucleic acid preparation prior to genome sequencing. Flow diagram describing the major protocol steps required for the purification of RoV and the amplification of RoV specific nucleic acid for next generation genome sequencing. Image of Illumina MiSeq obtained from https://assets.illumina.com/content/dam/illumina-marketing/images/systems/miseqdx/web-graphic-miseq-front-comparison-chart.jpg . Clipart image of pipette obtained from http://www.clker.com/clipart-pipette-with-tip.html . Clipart image of 96-well plate obtained from http://cyberuse.com/96-well-plate-template.html . Clipart image of Eppendorf tube obtained from http://www.clker.com/clipart-eppendorf-tube-with-open-cap-1.html and edited in Adobe Illustrator
    Figure Legend Snippet: The procedure for rotavirus capture and nucleic acid preparation prior to genome sequencing. Flow diagram describing the major protocol steps required for the purification of RoV and the amplification of RoV specific nucleic acid for next generation genome sequencing. Image of Illumina MiSeq obtained from https://assets.illumina.com/content/dam/illumina-marketing/images/systems/miseqdx/web-graphic-miseq-front-comparison-chart.jpg . Clipart image of pipette obtained from http://www.clker.com/clipart-pipette-with-tip.html . Clipart image of 96-well plate obtained from http://cyberuse.com/96-well-plate-template.html . Clipart image of Eppendorf tube obtained from http://www.clker.com/clipart-eppendorf-tube-with-open-cap-1.html and edited in Adobe Illustrator

    Techniques Used: Sequencing, Flow Cytometry, Purification, Amplification, Transferring

    Related Articles

    Next-Generation Sequencing:

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    Article Snippet: .. Issues with DNA sequencing must be acknowledged for both classical PCR and Illumina MiSeq sequencing (NGS). .. For DGGE‐analysis, these include nonequitable amplification, sequencing error and insufficient sequence length for accurate species identification.

    Sampling:

    Article Title: Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils
    Article Snippet: .. MiSeq sequencing of the 16S rRNA genes and their transcripts The microbial community structure in the different sampling points was assessed by Illumina MiSeq sequencing of the 16S rRNA genes and transcripts from the triplicate microcosms. ..

    Real-time Polymerase Chain Reaction:

    Article Title: Changes in rhizosphere microbial communities in potted cucumber seedlings treated with syringic acid
    Article Snippet: .. Both Illumina Miseq sequencing and real-time PCR showed that SA had inhibitory effect on Pseudomonas spp. in cucumber rhizosphere. .. In vitro experiment also confirmed that SA inhibited the growth of a strain of Pseudomonas spp. with antagonistic activity to FOC.

    Sequencing:

    Article Title: Changes in rhizosphere microbial communities in potted cucumber seedlings treated with syringic acid
    Article Snippet: .. Both Illumina Miseq sequencing and real-time PCR showed that SA had inhibitory effect on Pseudomonas spp. in cucumber rhizosphere. .. In vitro experiment also confirmed that SA inhibited the growth of a strain of Pseudomonas spp. with antagonistic activity to FOC.

    Article Title: Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils
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    Article Title: Saliva and tooth biofilm bacterial microbiota in adolescents in a low caries community
    Article Snippet: .. PacBio SMRT sequencing confirmed the results from Illumina MiSeq sequencing at the phylum and genus levels and partially at the species level, including the predominance of C. matruchotii in tooth biofilms. .. C. matruchotii was overlooked in many previous studies using PCR-based or metagenomic sequencing but was recognized as a prominent species in metatranscriptome , metaproteome , and spectral imaging fluorescence hybridization analyses.

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    Article Title: Somatic Mutation Screening Using Archival Formalin-Fixed, Paraffin-Embedded Tissues by Fluidigm Multiplex PCR and Illumina Sequencing
    Article Snippet: .. Supplemental Figure S5: Examples of somatic mutations detected by Fluidigm Access Array PCR and Illumina MiSeq sequencing. .. The aligned sequence reads are visualized using the Integrative Genomics Viewer (IGV).

    Article Title: Genotyping strategy matters when analyzing hypervariable major histocompatibility complex‐Experience from a passerine bird. Genotyping strategy matters when analyzing hypervariable major histocompatibility complex‐Experience from a passerine bird
    Article Snippet: .. The Norwegian Sequencing Center conducted the Illumina MiSeq sequencing. ..

    Article Title: Illumina sequencing‐based analysis of sediment bacteria community in different trophic status freshwater lakes
    Article Snippet: .. A total of 1,918,768 high quality sequences (average length 253 bp) were obtained by Illumina MiSeq sequencing at which the rarefaction curves of Shannon diversities approached a plateau, suggesting a complete capture of the bacterial community at each site. .. Based on a 97% sequence similarity cutoff, these sequences yielded a bacterial OTU number that ranged from 2279 to 4331 (Table ).

    Article Title: Bacterial communities associated with honeybee food stores are correlated with land use. Bacterial communities associated with honeybee food stores are correlated with land use
    Article Snippet: .. Issues with DNA sequencing must be acknowledged for both classical PCR and Illumina MiSeq sequencing (NGS). .. For DGGE‐analysis, these include nonequitable amplification, sequencing error and insufficient sequence length for accurate species identification.

    DNA Sequencing:

    Article Title: Bacterial communities associated with honeybee food stores are correlated with land use. Bacterial communities associated with honeybee food stores are correlated with land use
    Article Snippet: .. Issues with DNA sequencing must be acknowledged for both classical PCR and Illumina MiSeq sequencing (NGS). .. For DGGE‐analysis, these include nonequitable amplification, sequencing error and insufficient sequence length for accurate species identification.

    Polymerase Chain Reaction:

    Article Title: Somatic Mutation Screening Using Archival Formalin-Fixed, Paraffin-Embedded Tissues by Fluidigm Multiplex PCR and Illumina Sequencing
    Article Snippet: .. Supplemental Figure S3: Quality control (QC) at various steps of Fluidigm Access Array PCR and Illumina MiSeq sequencing. .. A: QC step 1: Assessment of preamplified products by conventional multiplex PCR and 10% polyacrylamide gel electrophoresis.

    Article Title: Somatic Mutation Screening Using Archival Formalin-Fixed, Paraffin-Embedded Tissues by Fluidigm Multiplex PCR and Illumina Sequencing
    Article Snippet: .. Supplemental Figure S5: Examples of somatic mutations detected by Fluidigm Access Array PCR and Illumina MiSeq sequencing. .. The aligned sequence reads are visualized using the Integrative Genomics Viewer (IGV).

    Article Title: Bacterial communities associated with honeybee food stores are correlated with land use. Bacterial communities associated with honeybee food stores are correlated with land use
    Article Snippet: .. Issues with DNA sequencing must be acknowledged for both classical PCR and Illumina MiSeq sequencing (NGS). .. For DGGE‐analysis, these include nonequitable amplification, sequencing error and insufficient sequence length for accurate species identification.

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    Illumina Inc miseq next generation sequencing platform
    Krona diagram depicting the fungal phyla identified in <t>Illumina</t> <t>MiSeq</t> analysis of (A) air conditioner ( n = 9) and (B) evaporative cooler ( n = 10) environments.
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    Image Search Results


    Krona diagram depicting the fungal phyla identified in Illumina MiSeq analysis of (A) air conditioner ( n = 9) and (B) evaporative cooler ( n = 10) environments.

    Journal: Environmental science. Processes & impacts

    Article Title: Microbial rRNA sequencing analysis of evaporative cooler indoor environments located in the Great Basin Desert region of the United States

    doi: 10.1039/c6em00413j

    Figure Lengend Snippet: Krona diagram depicting the fungal phyla identified in Illumina MiSeq analysis of (A) air conditioner ( n = 9) and (B) evaporative cooler ( n = 10) environments.

    Article Snippet: Fungal-specific qPCR has been used to assess the fungal populations in these air samples and these datasets are compared to data collected using the Illumina MiSeq next generation sequencing platform.

    Techniques:

    Most prevalent species within the fungal orders (A) Pleosporales and (B) Capnodiales identified in evaporative cooler environments ( n = 10) using Illumina MiSeq. Values are representative of the percentage of each species within each order.

    Journal: Environmental science. Processes & impacts

    Article Title: Microbial rRNA sequencing analysis of evaporative cooler indoor environments located in the Great Basin Desert region of the United States

    doi: 10.1039/c6em00413j

    Figure Lengend Snippet: Most prevalent species within the fungal orders (A) Pleosporales and (B) Capnodiales identified in evaporative cooler environments ( n = 10) using Illumina MiSeq. Values are representative of the percentage of each species within each order.

    Article Snippet: Fungal-specific qPCR has been used to assess the fungal populations in these air samples and these datasets are compared to data collected using the Illumina MiSeq next generation sequencing platform.

    Techniques:

    Donor specificity is maintained independent of experimental pipeline. ( a ) PCA bi-plots of clr transformed data on Illumina MiSeq and Ion Torrent PGM sequencing platforms. ( b ) Relative abundance profiles of individual subjects on each platform for top 20 families. ( c ) Relative abundances per platform represented as mean ± SD, with R 2 values displayed from linear model fitted to log10 values.

    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: Donor specificity is maintained independent of experimental pipeline. ( a ) PCA bi-plots of clr transformed data on Illumina MiSeq and Ion Torrent PGM sequencing platforms. ( b ) Relative abundance profiles of individual subjects on each platform for top 20 families. ( c ) Relative abundances per platform represented as mean ± SD, with R 2 values displayed from linear model fitted to log10 values.

    Article Snippet: All DNA samples were subjected to 16 S rRNA gene amplicon sequencing on two NGS platforms – Illumina MiSeq and Ion Torrent PGM.

    Techniques: Transformation Assay, 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: All DNA samples were subjected to 16 S rRNA gene amplicon sequencing on two NGS platforms – Illumina MiSeq and Ion Torrent PGM.

    Techniques: Sequencing

    Schematic overview of microbiome bioinformatic analysis workflow. The hypervariable V4 region of 16S rDNA from tick samples was sequenced and split by barcode with Illumina MiSeq. Resulting paired-end reads were joined and the primer region was removed. Reads were filtered by amplicon length and aligned to SILVA as the reference database. After removal of chimeras, reads were clustered into operational taxonomic units (OTU) and taxonomically classified. Finally, an OTU-table was created and results were visualized

    Journal: Parasites & Vectors

    Article Title: Combination of microbiome analysis and serodiagnostics to assess the risk of pathogen transmission by ticks to humans and animals in central Germany

    doi: 10.1186/s13071-018-3240-7

    Figure Lengend Snippet: Schematic overview of microbiome bioinformatic analysis workflow. The hypervariable V4 region of 16S rDNA from tick samples was sequenced and split by barcode with Illumina MiSeq. Resulting paired-end reads were joined and the primer region was removed. Reads were filtered by amplicon length and aligned to SILVA as the reference database. After removal of chimeras, reads were clustered into operational taxonomic units (OTU) and taxonomically classified. Finally, an OTU-table was created and results were visualized

    Article Snippet: All samples were diluted to the same molarity, pooled together, spiked with an internal control (15% PhiX) and paired-end sequenced on the MiSeq Illumina platform using a flow cell with V2 chemistry (500 cycles).

    Techniques: Amplification

    Individual differences at the species level in chronic T. gondii -infected and healthy mice of the first cohort. CD1 mice were infected IP with 500 T. gondii tachyzoites (GT1) in PBS, along with 5 control CD1 mice by the IP route with PBS only. The group was sacrificed at 5 mpi. Whole 16S rDNA libraries were sequenced using the MiSeq Illumina sequencing platform to profile small intestinal microbiome. Sequences were analyzed using QIIME pipeline focusing on the v3-v4 region. The graph shows (a) the log-transformed average of highly variable species in infected and control groups and (b) the percentage of highly variable species of the upper intestinal microflora in each mouse. Highly variable species only appeared in the infected mice and the vast majority of them belonged to the Firmicutes phyla.

    Journal: Scientifica

    Article Title: Toxoplasma gondii-Induced Long-Term Changes in the Upper Intestinal Microflora during the Chronic Stage of Infection

    doi: 10.1155/2018/2308619

    Figure Lengend Snippet: Individual differences at the species level in chronic T. gondii -infected and healthy mice of the first cohort. CD1 mice were infected IP with 500 T. gondii tachyzoites (GT1) in PBS, along with 5 control CD1 mice by the IP route with PBS only. The group was sacrificed at 5 mpi. Whole 16S rDNA libraries were sequenced using the MiSeq Illumina sequencing platform to profile small intestinal microbiome. Sequences were analyzed using QIIME pipeline focusing on the v3-v4 region. The graph shows (a) the log-transformed average of highly variable species in infected and control groups and (b) the percentage of highly variable species of the upper intestinal microflora in each mouse. Highly variable species only appeared in the infected mice and the vast majority of them belonged to the Firmicutes phyla.

    Article Snippet: Sequencing was performed on the MiSeq Illumina sequencing platform using a 2 × 300 PE sequencing reagent kit (Cat # MS-102-3003 Illumina, San Diego, CA).

    Techniques: Infection, Mouse Assay, Sequencing, Transformation Assay

    Individual differences at species level in acute T. gondii -infected and healthy mice of the first cohort. 5 CD1 mice were infected IP with 500 T. gondii tachyzoites (GT1) in PBS, along with 5 control CD1 mice by the IP route with PBS only. The group was sacrificed at 5 dpi. Whole 16S rDNA libraries were sequenced using the MiSeq Illumina sequencing platform to profile small intestinal microbiome. Sequences were analyzed using QIIME pipeline focusing on the v3-v4 region. The graph shows (a) the log-transformed ratios of averaged standard deviation of the relative abundance of highly variable species in infected and control mice and (b) the percentage of highly variable species of the upper intestinal microflora in each mouse. Lactobacillus, Proteus, and Bacteroidetes species are increasingly unstable in the acute infected mice, while Bacillaceae species appear unstable in the uninfected mice.

    Journal: Scientifica

    Article Title: Toxoplasma gondii-Induced Long-Term Changes in the Upper Intestinal Microflora during the Chronic Stage of Infection

    doi: 10.1155/2018/2308619

    Figure Lengend Snippet: Individual differences at species level in acute T. gondii -infected and healthy mice of the first cohort. 5 CD1 mice were infected IP with 500 T. gondii tachyzoites (GT1) in PBS, along with 5 control CD1 mice by the IP route with PBS only. The group was sacrificed at 5 dpi. Whole 16S rDNA libraries were sequenced using the MiSeq Illumina sequencing platform to profile small intestinal microbiome. Sequences were analyzed using QIIME pipeline focusing on the v3-v4 region. The graph shows (a) the log-transformed ratios of averaged standard deviation of the relative abundance of highly variable species in infected and control mice and (b) the percentage of highly variable species of the upper intestinal microflora in each mouse. Lactobacillus, Proteus, and Bacteroidetes species are increasingly unstable in the acute infected mice, while Bacillaceae species appear unstable in the uninfected mice.

    Article Snippet: Sequencing was performed on the MiSeq Illumina sequencing platform using a 2 × 300 PE sequencing reagent kit (Cat # MS-102-3003 Illumina, San Diego, CA).

    Techniques: Infection, Mouse Assay, Sequencing, Transformation Assay, Standard Deviation

    Individual differences at phylum level in chronically T. gondii infected and healthy mice of the second cohort. 45 CD1 mice were infected IP with 500 T. gondii tachyzoites (GT1) in PBS, along with 17 control CD1 mice by the IP route with PBS only. The group was sacrificed at 5 mpi. Whole 16S rDNA libraries were sequenced using the MiSeq Illumina sequencing platform to profile the small intestinal microbiome. Sequences were analyzed using QIIME 2 pipeline focusing on the v3-v4 region. The graph shows enrichment of Bacteroidetes phylum in chronically infected mice.

    Journal: Scientifica

    Article Title: Toxoplasma gondii-Induced Long-Term Changes in the Upper Intestinal Microflora during the Chronic Stage of Infection

    doi: 10.1155/2018/2308619

    Figure Lengend Snippet: Individual differences at phylum level in chronically T. gondii infected and healthy mice of the second cohort. 45 CD1 mice were infected IP with 500 T. gondii tachyzoites (GT1) in PBS, along with 17 control CD1 mice by the IP route with PBS only. The group was sacrificed at 5 mpi. Whole 16S rDNA libraries were sequenced using the MiSeq Illumina sequencing platform to profile the small intestinal microbiome. Sequences were analyzed using QIIME 2 pipeline focusing on the v3-v4 region. The graph shows enrichment of Bacteroidetes phylum in chronically infected mice.

    Article Snippet: Sequencing was performed on the MiSeq Illumina sequencing platform using a 2 × 300 PE sequencing reagent kit (Cat # MS-102-3003 Illumina, San Diego, CA).

    Techniques: Infection, Mouse Assay, Sequencing