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Illumina Inc illumina sequencing machine
Prevalence, causes, and effects of cross-contamination in miRNA-seq data. a Percentages of public mouse, nematode, and fly datasets that contain primate sequences (putative human contamination). b Percentages of primate sequences in putatively contaminated datasets (considering only clade-specific sequences). The white dot indicates the median value, the thick black line indicates the range from 25 to 75% percentiles, and the whole gray area indicates the range from 5 to 95% percentiles. c Human and mouse samples were profiled in parallel with <t>Illumina</t> sequencing to detect sources of cross-contamination (top). Using the Illumina default settings for sample assignment, rodent contamination was detected in all nine human samples. Each bar represents one sample, and the numbers in each bar indicate the number of contaminating sequences (bars below). d Using more stringent settings for sample assignment, only sequences with perfect matches to known sample indices were retained (top). This computational step removed most rodent contaminations (bottom). e In an additional filtering step, sequences with inconsistent indices were discarded (top), removing contaminations completely from six out of nine human samples (bottom). f Mouse samples in silico contaminated with controlled abundances of human or fly sequences ranging from 0 to 100% (top). Principal component analyses (PCA) show how the overall miRNA composition of the sample changes with increasing levels of contamination (bottom). g Effects of the contaminations from ( f ) on gene differential expression (DE) analyses. Sensitivity, specificity, and accuracy (in shades of brown) are given as fractions, while the false positive rates (in red) are absolute numbers. h Effects of contamination on the prediction of novel miRNAs
Illumina Sequencing Machine, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 9139 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/illumina sequencing machine/product/Illumina Inc
Average 88 stars, based on 9139 article reviews
Price from $9.99 to $1999.99
illumina sequencing machine - by Bioz Stars, 2020-08
88/100 stars

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1) Product Images from "miRTrace reveals the organismal origins of microRNA sequencing data"

Article Title: miRTrace reveals the organismal origins of microRNA sequencing data

Journal: Genome Biology

doi: 10.1186/s13059-018-1588-9

Prevalence, causes, and effects of cross-contamination in miRNA-seq data. a Percentages of public mouse, nematode, and fly datasets that contain primate sequences (putative human contamination). b Percentages of primate sequences in putatively contaminated datasets (considering only clade-specific sequences). The white dot indicates the median value, the thick black line indicates the range from 25 to 75% percentiles, and the whole gray area indicates the range from 5 to 95% percentiles. c Human and mouse samples were profiled in parallel with Illumina sequencing to detect sources of cross-contamination (top). Using the Illumina default settings for sample assignment, rodent contamination was detected in all nine human samples. Each bar represents one sample, and the numbers in each bar indicate the number of contaminating sequences (bars below). d Using more stringent settings for sample assignment, only sequences with perfect matches to known sample indices were retained (top). This computational step removed most rodent contaminations (bottom). e In an additional filtering step, sequences with inconsistent indices were discarded (top), removing contaminations completely from six out of nine human samples (bottom). f Mouse samples in silico contaminated with controlled abundances of human or fly sequences ranging from 0 to 100% (top). Principal component analyses (PCA) show how the overall miRNA composition of the sample changes with increasing levels of contamination (bottom). g Effects of the contaminations from ( f ) on gene differential expression (DE) analyses. Sensitivity, specificity, and accuracy (in shades of brown) are given as fractions, while the false positive rates (in red) are absolute numbers. h Effects of contamination on the prediction of novel miRNAs
Figure Legend Snippet: Prevalence, causes, and effects of cross-contamination in miRNA-seq data. a Percentages of public mouse, nematode, and fly datasets that contain primate sequences (putative human contamination). b Percentages of primate sequences in putatively contaminated datasets (considering only clade-specific sequences). The white dot indicates the median value, the thick black line indicates the range from 25 to 75% percentiles, and the whole gray area indicates the range from 5 to 95% percentiles. c Human and mouse samples were profiled in parallel with Illumina sequencing to detect sources of cross-contamination (top). Using the Illumina default settings for sample assignment, rodent contamination was detected in all nine human samples. Each bar represents one sample, and the numbers in each bar indicate the number of contaminating sequences (bars below). d Using more stringent settings for sample assignment, only sequences with perfect matches to known sample indices were retained (top). This computational step removed most rodent contaminations (bottom). e In an additional filtering step, sequences with inconsistent indices were discarded (top), removing contaminations completely from six out of nine human samples (bottom). f Mouse samples in silico contaminated with controlled abundances of human or fly sequences ranging from 0 to 100% (top). Principal component analyses (PCA) show how the overall miRNA composition of the sample changes with increasing levels of contamination (bottom). g Effects of the contaminations from ( f ) on gene differential expression (DE) analyses. Sensitivity, specificity, and accuracy (in shades of brown) are given as fractions, while the false positive rates (in red) are absolute numbers. h Effects of contamination on the prediction of novel miRNAs

Techniques Used: Sequencing, In Silico, Expressing

2) Product Images from "miRTrace reveals the organismal origins of microRNA sequencing data"

Article Title: miRTrace reveals the organismal origins of microRNA sequencing data

Journal: Genome Biology

doi: 10.1186/s13059-018-1588-9

Prevalence, causes, and effects of cross-contamination in miRNA-seq data. a Percentages of public mouse, nematode, and fly datasets that contain primate sequences (putative human contamination). b Percentages of primate sequences in putatively contaminated datasets (considering only clade-specific sequences). The white dot indicates the median value, the thick black line indicates the range from 25 to 75% percentiles, and the whole gray area indicates the range from 5 to 95% percentiles. c Human and mouse samples were profiled in parallel with Illumina sequencing to detect sources of cross-contamination (top). Using the Illumina default settings for sample assignment, rodent contamination was detected in all nine human samples. Each bar represents one sample, and the numbers in each bar indicate the number of contaminating sequences (bars below). d Using more stringent settings for sample assignment, only sequences with perfect matches to known sample indices were retained (top). This computational step removed most rodent contaminations (bottom). e In an additional filtering step, sequences with inconsistent indices were discarded (top), removing contaminations completely from six out of nine human samples (bottom). f Mouse samples in silico contaminated with controlled abundances of human or fly sequences ranging from 0 to 100% (top). Principal component analyses (PCA) show how the overall miRNA composition of the sample changes with increasing levels of contamination (bottom). g Effects of the contaminations from ( f ) on gene differential expression (DE) analyses. Sensitivity, specificity, and accuracy (in shades of brown) are given as fractions, while the false positive rates (in red) are absolute numbers. h Effects of contamination on the prediction of novel miRNAs
Figure Legend Snippet: Prevalence, causes, and effects of cross-contamination in miRNA-seq data. a Percentages of public mouse, nematode, and fly datasets that contain primate sequences (putative human contamination). b Percentages of primate sequences in putatively contaminated datasets (considering only clade-specific sequences). The white dot indicates the median value, the thick black line indicates the range from 25 to 75% percentiles, and the whole gray area indicates the range from 5 to 95% percentiles. c Human and mouse samples were profiled in parallel with Illumina sequencing to detect sources of cross-contamination (top). Using the Illumina default settings for sample assignment, rodent contamination was detected in all nine human samples. Each bar represents one sample, and the numbers in each bar indicate the number of contaminating sequences (bars below). d Using more stringent settings for sample assignment, only sequences with perfect matches to known sample indices were retained (top). This computational step removed most rodent contaminations (bottom). e In an additional filtering step, sequences with inconsistent indices were discarded (top), removing contaminations completely from six out of nine human samples (bottom). f Mouse samples in silico contaminated with controlled abundances of human or fly sequences ranging from 0 to 100% (top). Principal component analyses (PCA) show how the overall miRNA composition of the sample changes with increasing levels of contamination (bottom). g Effects of the contaminations from ( f ) on gene differential expression (DE) analyses. Sensitivity, specificity, and accuracy (in shades of brown) are given as fractions, while the false positive rates (in red) are absolute numbers. h Effects of contamination on the prediction of novel miRNAs

Techniques Used: Sequencing, In Silico, Expressing

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Concentration Assay:

Article Title: Cucumber (Cucumis sativus L.) Seedling Rhizosphere Trichoderma and Fusarium spp. Communities Altered by Vanillic Acid
Article Snippet: .. Illumina MiSeq Sequencing of Fungal Communities previously found that in a continuous monocropping system, the concentration of vanillic acid in the cucumber rhizosphere was approximately 0.05 μmol g-1 soil. .. Thus, we performed an assessment of fungal communities through Illumina MiSeq sequencing of the total soil DNA obtained from the 0 and 0.05 μmol g-1 soil VA treatments.

Next-Generation 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.

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: 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.

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: 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.

Article Title: Cucumber (Cucumis sativus L.) Seedling Rhizosphere Trichoderma and Fusarium spp. Communities Altered by Vanillic Acid
Article Snippet: .. Illumina MiSeq Sequencing of Fungal Communities previously found that in a continuous monocropping system, the concentration of vanillic acid in the cucumber rhizosphere was approximately 0.05 μmol g-1 soil. .. Thus, we performed an assessment of fungal communities through Illumina MiSeq sequencing of the total soil DNA obtained from the 0 and 0.05 μmol g-1 soil VA treatments.

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 nextseq500 high throughput sequencing machine
    Nextseq500 High Throughput Sequencing Machine, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nextseq500 high throughput sequencing machine/product/Illumina Inc
    Average 91 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nextseq500 high throughput sequencing machine - by Bioz Stars, 2020-08
    91/100 stars
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