ion xpress barcode adapters  (Thermo Fisher)


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    Structured Review

    Thermo Fisher ion xpress barcode adapters
    Ion Xpress Barcode Adapters, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ion xpress barcode adapters/product/Thermo Fisher
    Average 97 stars, based on 40 article reviews
    Price from $9.99 to $1999.99
    ion xpress barcode adapters - by Bioz Stars, 2022-10
    97/100 stars

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  • 96
    Thermo Fisher ion xpress barcode adapters 1 96 kit
    Schematic overview of the MTA-seq workflow used in this study. Primer pairs (443) were designed to generate amplicons harboring one known SNP. Highly multiplexed PCR was conducted with the TaKaRa multiplex PCR amplification kit version 2. Amplicons were end-repaired, adapter-ligated, and nick-repaired with the SPARK DNA sample prep kit for Ion Torrent. To identify individual samples, the Ion <t>Xpress</t> <t>Barcode</t> Adapters 1-96 kit was adopted to add index adapters. The barcoded library was sequenced on an Ion Proton sequencer. SNPs were called by using the “mpileup2cns” command of the VarScan software.
    Ion Xpress Barcode Adapters 1 96 Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ion xpress barcode adapters 1 96 kit/product/Thermo Fisher
    Average 96 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ion xpress barcode adapters 1 96 kit - by Bioz Stars, 2022-10
    96/100 stars
      Buy from Supplier

    92
    Thermo Fisher ion xpress barcode
    Comparison of RNA editing ratios between the cerebral cortex and spleen of WT mice. ( A ) The protocol to create Ion amplicon libraries for the evaluation of RNA editing ratios at multiple sites. After reverse-transcription using oligo(dT) primers or random hexamers, the first PCR was performed using cDNA (in green) that included an RNA editing site (shown as a red cross) and first primers specific for each editing site (in yellow). Then, a second round of PCR was performed using an aliquot of the first PCR product as a template, with each second forward primer specific to the editing site and containing an A adaptor (in light green), an Ion <t>Xpress</t> <t>Barcode™</t> (in gray) and editing site-specific sequences (in brown), and a reverse primer that contained a trP1 adaptor (in light blue); editing site-specific sequences (in brown) were also included. All second PCR products were designed to be 190 to 200 bp in length. After 50–300 PCR products were combined, the samples were sequenced using an Ion Torrent™ Personal Genome Machine™ (Ion PGM) system. ( B ) Immunoblot analysis of adenosine deaminase acting on RNA (ADAR)1 p110, ADAR1 p150 and ADAR2 expression in cerebral cortexes and spleens isolated from wild-type (WT), Adar1 E861A/E861A Ifih −/− mice (Adar1 KI) and Adar2 −/− Gria2 R/R (Adar2 KO) mice (n=2 mice for each group). The expression of GAPDH is shown as a reference. ( C ) Validation of the methodology by referring to the editing ratios of known ADAR1 (AZIN1 serine/glycine [S/G]) and ADAR2 sites (Kv1.1 isoleucine/valine [I/V]). Editing ratios at each site in each indicated tissue isolated from WT, Adar1 KI and Adar KO mice are displayed as the mean ± SEM (n=3 mice for each group; Student’s t -test, * p
    Ion Xpress Barcode, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ion xpress barcode/product/Thermo Fisher
    Average 92 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ion xpress barcode - by Bioz Stars, 2022-10
    92/100 stars
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    97
    Thermo Fisher ion xpress barcode adapters kits
    Focus on Parabacteroides distasonis . A) Relation between P. distasonis log‐fold change and intraindividuals Bray–Curtis dissimilarity, considering only individuals from the RD group carrying P. distasonis ( n = 21). Spearman's coefficient along with the associated p ‐value are displayed. B) <t>Barcode</t> of P. distasonis in the RD group (left) or in the CP group (right), at baseline (top) or at D42 (bottom). The 50 “tracer” genes are in rows, abundance is indicated by color gradient (white, not detected; red, most abundant); individuals, ordered by increasing MGS richness, are in columns. The lowest bar gives the log‐fold change between baseline and D42 associated with each individual (i.e., each column). C) Difference in P. distasonis log‐fold change when comparing individuals from the RD group whose P. distasonis strain carries a specific gene annotated as SusD ( n = 10) with individuals whose strain does not have this gene ( n = 11). CP indicates control product; log2FC, log‐fold change; MGS, MetaGenomic species; RD, resistant dextrin.
    Ion Xpress Barcode Adapters Kits, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ion xpress barcode adapters kits/product/Thermo Fisher
    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ion xpress barcode adapters kits - by Bioz Stars, 2022-10
    97/100 stars
      Buy from Supplier

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    Schematic overview of the MTA-seq workflow used in this study. Primer pairs (443) were designed to generate amplicons harboring one known SNP. Highly multiplexed PCR was conducted with the TaKaRa multiplex PCR amplification kit version 2. Amplicons were end-repaired, adapter-ligated, and nick-repaired with the SPARK DNA sample prep kit for Ion Torrent. To identify individual samples, the Ion Xpress Barcode Adapters 1-96 kit was adopted to add index adapters. The barcoded library was sequenced on an Ion Proton sequencer. SNPs were called by using the “mpileup2cns” command of the VarScan software.

    Journal: Frontiers in Plant Science

    Article Title: Multiplex PCR Targeted Amplicon Sequencing (MTA-Seq): Simple, Flexible, and Versatile SNP Genotyping by Highly Multiplexed PCR Amplicon Sequencing

    doi: 10.3389/fpls.2018.00201

    Figure Lengend Snippet: Schematic overview of the MTA-seq workflow used in this study. Primer pairs (443) were designed to generate amplicons harboring one known SNP. Highly multiplexed PCR was conducted with the TaKaRa multiplex PCR amplification kit version 2. Amplicons were end-repaired, adapter-ligated, and nick-repaired with the SPARK DNA sample prep kit for Ion Torrent. To identify individual samples, the Ion Xpress Barcode Adapters 1-96 kit was adopted to add index adapters. The barcoded library was sequenced on an Ion Proton sequencer. SNPs were called by using the “mpileup2cns” command of the VarScan software.

    Article Snippet: For library preparation, we used the SPARK DNA sample prep kit for Ion Torrent (Enzymatics, Beverly, MA, USA) with an Ion Xpress Barcode Adapters 1–96 kit (Thermo Fisher Scientific K.K.), and size selection was performed using E-Gel SizeSelect (Thermo Fisher Scientific K.K.) according to manufacturer instructions.

    Techniques: Polymerase Chain Reaction, Multiplex Assay, Amplification, Sample Prep, Software

    Comparison of RNA editing ratios between the cerebral cortex and spleen of WT mice. ( A ) The protocol to create Ion amplicon libraries for the evaluation of RNA editing ratios at multiple sites. After reverse-transcription using oligo(dT) primers or random hexamers, the first PCR was performed using cDNA (in green) that included an RNA editing site (shown as a red cross) and first primers specific for each editing site (in yellow). Then, a second round of PCR was performed using an aliquot of the first PCR product as a template, with each second forward primer specific to the editing site and containing an A adaptor (in light green), an Ion Xpress Barcode™ (in gray) and editing site-specific sequences (in brown), and a reverse primer that contained a trP1 adaptor (in light blue); editing site-specific sequences (in brown) were also included. All second PCR products were designed to be 190 to 200 bp in length. After 50–300 PCR products were combined, the samples were sequenced using an Ion Torrent™ Personal Genome Machine™ (Ion PGM) system. ( B ) Immunoblot analysis of adenosine deaminase acting on RNA (ADAR)1 p110, ADAR1 p150 and ADAR2 expression in cerebral cortexes and spleens isolated from wild-type (WT), Adar1 E861A/E861A Ifih −/− mice (Adar1 KI) and Adar2 −/− Gria2 R/R (Adar2 KO) mice (n=2 mice for each group). The expression of GAPDH is shown as a reference. ( C ) Validation of the methodology by referring to the editing ratios of known ADAR1 (AZIN1 serine/glycine [S/G]) and ADAR2 sites (Kv1.1 isoleucine/valine [I/V]). Editing ratios at each site in each indicated tissue isolated from WT, Adar1 KI and Adar KO mice are displayed as the mean ± SEM (n=3 mice for each group; Student’s t -test, * p

    Journal: bioRxiv

    Article Title: A comparative analysis among ADAR mutant mice reveals site-specific regulation of RNA editing

    doi: 10.1101/822916

    Figure Lengend Snippet: Comparison of RNA editing ratios between the cerebral cortex and spleen of WT mice. ( A ) The protocol to create Ion amplicon libraries for the evaluation of RNA editing ratios at multiple sites. After reverse-transcription using oligo(dT) primers or random hexamers, the first PCR was performed using cDNA (in green) that included an RNA editing site (shown as a red cross) and first primers specific for each editing site (in yellow). Then, a second round of PCR was performed using an aliquot of the first PCR product as a template, with each second forward primer specific to the editing site and containing an A adaptor (in light green), an Ion Xpress Barcode™ (in gray) and editing site-specific sequences (in brown), and a reverse primer that contained a trP1 adaptor (in light blue); editing site-specific sequences (in brown) were also included. All second PCR products were designed to be 190 to 200 bp in length. After 50–300 PCR products were combined, the samples were sequenced using an Ion Torrent™ Personal Genome Machine™ (Ion PGM) system. ( B ) Immunoblot analysis of adenosine deaminase acting on RNA (ADAR)1 p110, ADAR1 p150 and ADAR2 expression in cerebral cortexes and spleens isolated from wild-type (WT), Adar1 E861A/E861A Ifih −/− mice (Adar1 KI) and Adar2 −/− Gria2 R/R (Adar2 KO) mice (n=2 mice for each group). The expression of GAPDH is shown as a reference. ( C ) Validation of the methodology by referring to the editing ratios of known ADAR1 (AZIN1 serine/glycine [S/G]) and ADAR2 sites (Kv1.1 isoleucine/valine [I/V]). Editing ratios at each site in each indicated tissue isolated from WT, Adar1 KI and Adar KO mice are displayed as the mean ± SEM (n=3 mice for each group; Student’s t -test, * p

    Article Snippet: A second round of PCR was then performed using an aliquot of the first PCR product as a template and second primers that were editing-site specific; an A adaptor (5’-CCATCTCATCCCTGCGTGTCTCCGACTCAG-3’), an Ion Xpress Barcode™ and a trP1 adaptor (5’-CCTCTCTATGGGCAGTCGGTGAT-3’) were in forward and reverse primers, respectively ( and Supplemental Table S6).

    Techniques: Mouse Assay, Amplification, Polymerase Chain Reaction, Expressing, Isolation

    Focus on Parabacteroides distasonis . A) Relation between P. distasonis log‐fold change and intraindividuals Bray–Curtis dissimilarity, considering only individuals from the RD group carrying P. distasonis ( n = 21). Spearman's coefficient along with the associated p ‐value are displayed. B) Barcode of P. distasonis in the RD group (left) or in the CP group (right), at baseline (top) or at D42 (bottom). The 50 “tracer” genes are in rows, abundance is indicated by color gradient (white, not detected; red, most abundant); individuals, ordered by increasing MGS richness, are in columns. The lowest bar gives the log‐fold change between baseline and D42 associated with each individual (i.e., each column). C) Difference in P. distasonis log‐fold change when comparing individuals from the RD group whose P. distasonis strain carries a specific gene annotated as SusD ( n = 10) with individuals whose strain does not have this gene ( n = 11). CP indicates control product; log2FC, log‐fold change; MGS, MetaGenomic species; RD, resistant dextrin.

    Journal: Molecular Nutrition & Food Research

    Article Title: Diet Supplementation with NUTRIOSE, a Resistant Dextrin, Increases the Abundance of Parabacteroides distasonis in the Human Gut, Diet Supplementation with NUTRIOSE, a Resistant Dextrin, Increases the Abundance of Parabacteroides distasonis in the Human Gut

    doi: 10.1002/mnfr.202101091

    Figure Lengend Snippet: Focus on Parabacteroides distasonis . A) Relation between P. distasonis log‐fold change and intraindividuals Bray–Curtis dissimilarity, considering only individuals from the RD group carrying P. distasonis ( n = 21). Spearman's coefficient along with the associated p ‐value are displayed. B) Barcode of P. distasonis in the RD group (left) or in the CP group (right), at baseline (top) or at D42 (bottom). The 50 “tracer” genes are in rows, abundance is indicated by color gradient (white, not detected; red, most abundant); individuals, ordered by increasing MGS richness, are in columns. The lowest bar gives the log‐fold change between baseline and D42 associated with each individual (i.e., each column). C) Difference in P. distasonis log‐fold change when comparing individuals from the RD group whose P. distasonis strain carries a specific gene annotated as SusD ( n = 10) with individuals whose strain does not have this gene ( n = 11). CP indicates control product; log2FC, log‐fold change; MGS, MetaGenomic species; RD, resistant dextrin.

    Article Snippet: Shearing of DNA into fragments of approximately 150 bp was performed using an ultrasonicator (Covaris, Woburn, MA, USA) and DNA fragment library construction was performed using the Ion Plus Fragment Library and Ion Xpress Barcode Adapters Kits (ThermoFisher Scientific, Waltham, MA, USA).

    Techniques: