Sequencing:Article Title: Structural, functional, resistome and pathogenicity profiling of the Cooum river.
Article Snippet: The microbial community’s structure and functions determine the health, quality, and anthropogenic conditions of the river ecosystems.. The presence of Bacteria such as Arcobacter spp, Escherichia spp, and Campylobacters spp, have been shown to reflect the poor water quality of rivers.. Apprehension of the microbial community in polluted water bodies is significant because it affects human health and the environment.
Article Title: Genomic characterisation and epidemiology of nosocomial Serratia marcescens isolates resistant to ceftazidime and their plasmids mediating rare bla TEM-61 .
Article Snippet: Genomic DNA was extracted using a Wizard® enomic DNA Purification Kit (Promega, Madison, WI, USA). .. A lirary was prepared using an NEBNext® Ultra DNA Library Prep it (New England Biolabs, Ipswich, MA, USA), and 150-bp pairednd sequencing was performed using a NovaSeq 60 0 0 platform Illumina Inc., San Diego, CA, USA). .. Genome assembly was perormed de novo using the A5-miseq pipeline v.20160825.
Article Title: Biotyping reveals loss of motility in two distinct Yersinia ruckeri lineages exclusive to Norwegian aquaculture
Article Snippet: Of these, seven were downloaded from the National Center for Biotechnology Information (NCBI), while the remaining 19 were generated as described below. .. Sequencing libraries were prepared by use of either NEBNext Ultra DNA Library Prep‐ (New England Biolabs, Ipswich, MA, USA), TruSeq DNA PCR‐Free‐ (Illumina, San Diego, CA, USA) or NexteraFlex‐ (Illumina, San Diego, CA, USA) kits. .. Subsequent Illumina sequencing was performed on either a HiSeq or MiSeq platform, with paired end read lengths of 125, 150 or 300 base pairs.
Amplification:Article Title: Structural, functional, resistome and pathogenicity profiling of the Cooum river.
Article Snippet: The microbial community’s structure and functions determine the health, quality, and anthropogenic conditions of the river ecosystems.. The presence of Bacteria such as Arcobacter spp, Escherichia spp, and Campylobacters spp, have been shown to reflect the poor water quality of rivers.. Apprehension of the microbial community in polluted water bodies is significant because it affects human health and the environment.
Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double‐distilled water using an M220 Focused‐ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead‐based size selection; (3) size selection (~400–600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size‐selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double- distilled water using an M220 Focused- ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead- based size selection; (3) size selection (~400– 600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size- selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Adapter Ligation:Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double‐distilled water using an M220 Focused‐ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead‐based size selection; (3) size selection (~400–600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size‐selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double- distilled water using an M220 Focused- ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead- based size selection; (3) size selection (~400– 600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size- selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Polymerase Chain Reaction:Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double‐distilled water using an M220 Focused‐ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead‐based size selection; (3) size selection (~400–600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size‐selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Article Title: Biotyping reveals loss of motility in two distinct Yersinia ruckeri lineages exclusive to Norwegian aquaculture
Article Snippet: Of these, seven were downloaded from the National Center for Biotechnology Information (NCBI), while the remaining 19 were generated as described below. .. Sequencing libraries were prepared by use of either NEBNext Ultra DNA Library Prep‐ (New England Biolabs, Ipswich, MA, USA), TruSeq DNA PCR‐Free‐ (Illumina, San Diego, CA, USA) or NexteraFlex‐ (Illumina, San Diego, CA, USA) kits. .. Subsequent Illumina sequencing was performed on either a HiSeq or MiSeq platform, with paired end read lengths of 125, 150 or 300 base pairs.
Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double- distilled water using an M220 Focused- ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead- based size selection; (3) size selection (~400– 600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size- selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Purification:Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double‐distilled water using an M220 Focused‐ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead‐based size selection; (3) size selection (~400–600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size‐selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double- distilled water using an M220 Focused- ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead- based size selection; (3) size selection (~400– 600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size- selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Size Selection:Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double‐distilled water using an M220 Focused‐ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead‐based size selection; (3) size selection (~400–600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size‐selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double- distilled water using an M220 Focused- ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead- based size selection; (3) size selection (~400– 600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size- selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Selection:Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double‐distilled water using an M220 Focused‐ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead‐based size selection; (3) size selection (~400–600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size‐selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double- distilled water using an M220 Focused- ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead- based size selection; (3) size selection (~400– 600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size- selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Multiplex Assay:Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double‐distilled water using an M220 Focused‐ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead‐based size selection; (3) size selection (~400–600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size‐selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
Article Title: Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.
Article Snippet: Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Venlo, Netherlands). .. Between 200 ng and 1 μg of extracted DNA was sheared in 50 μL of double- distilled water using an M220 Focused- ultrasonicator (Covaris, Woburn, Massachusetts, USA) with the program for fragmentation to 500 bp for 25 s. Library preparation was performed using the NEBNext Ultra DNA Library Prep (New England Biolabs, Ipswich, Massachusetts, USA) protocol for Illumina with a few modifications: (1) a half volume of the samples and NEBNext chemicals were used during library preparation; (2) one additional cleanup step was implemented after the adapter ligation, for which a QIAquick PCR Purification Kit (QIAGEN) was used to clean residual nucleotides, enzymes, and salts from the DNA fragments as a prerequisite for efficient bead- based size selection; (3) size selection (~400– 600 bp) was performed using SPRIselect beads (Beckman Coulter, Brea, California, USA) with the ratio 0.65× for the left side and 0.55× for the right side selection, and amplification of the ligated size- selected fragments was performed with eight cycles of PCR, using NEBNext Multiplex Oligos for Illumina Index Primers Set 1 and 2 (New England Biolabs) or Dual Index Set 1 (New England Biolabs); (4) enriched PCR products were cleaned twice with Agencourt AMPure XP beads (Beckman Coulter) with the ratios 0.75× and 0.7×. ..
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