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Illumina Inc truseq sbs kit v3 hs
Truseq Sbs Kit V3 Hs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 82 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/truseq sbs kit v3 hs/product/Illumina Inc
Average 99 stars, based on 82 article reviews
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truseq sbs kit v3 hs - by Bioz Stars, 2020-02
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Related Articles

DNA Extraction:

Article Title: Deciphering the Genetic Blueprint behind Holstein Milk Proteins and Production
Article Snippet: DNA was isolated from whole blood using a G-DEXTMIIb Genomic DNA Extraction Kit (iNtRoN Biotechnology, Seoul, Korea) according to the manufacturer’s protocol. .. Paired-end sequencing was conducted with NICEM (National Instrumentation Center for Environmental Management, Seoul, Korea) using the Illumina HiSeq2000 platform with TruSeq SBS Kit v3-HS (Illumina).

Amplification:

Article Title: Deciphering the Genetic Blueprint behind Holstein Milk Proteins and Production
Article Snippet: The fragments of sheared DNA were end-repaired, A-tailed, adaptor ligated, and amplified using a TruSeq DNA Sample Prep. .. Paired-end sequencing was conducted with NICEM (National Instrumentation Center for Environmental Management, Seoul, Korea) using the Illumina HiSeq2000 platform with TruSeq SBS Kit v3-HS (Illumina).

Article Title: Natural Variation of Molecular and Morphological Gibberellin Responses 1Natural Variation of Molecular and Morphological Gibberellin Responses 1 [OPEN]
Article Snippet: .. After quality control using the 2100 Bioanalyzer, clusters were generated through amplification using the TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina) followed by sequencing on a Illumina HiSeq 2000 with the TruSeq SBS Kit v3-HS (Illumina). .. Sequencing was performed in paired-end mode with a read length of 50 bp.

Article Title: Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum
Article Snippet: The resulting di-tagged cDNA was amplified by PCR using primers that anneal to the two different tagging sequences on the cDNA to generate the library. .. Sequencing was done on the HiSeq 2500 (Illumina, San Diego, CA, USA) using TruSeq SBS Kit v3 – HS (Illumina, San Diego, CA, USA) for 50 cycles.

Construct:

Article Title: Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus
Article Snippet: RNA-seq libraries were constructed using NEBNext RNA sample preparation kit (NEB) in accordance with the standard low-throughput protocol. .. Samples were sequenced in a 1×100 nt way on an Illumina Hiseq2500 instrument using the TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina).

Article Title: Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge
Article Snippet: To construct the libraries for whole-genome sequencing, DNA was processed using a TruSeq DNA Sample Preparation kit v.2 (Illumina, San Diego, CA) according to the manufacturer’s instructions. .. Diluted libraries were clustered using a cBot instrument (Illumina) with a TruSeq PE Cluster Kit v3 (Illumina) and sequenced using a HiSeq 2000 sequencer (Illumina) with TruSeq SBS Kit v3-HS (Illumina), read length 101 from each end.

Real-time Polymerase Chain Reaction:

Article Title: Role of UHRF1 in de novo DNA methylation in oocytes and maintenance methylation in preimplantation embryos
Article Snippet: The concentrations of the PBAT libraries were measured by a qPCR using a KAPA Illumina Library Quantification kit (Kapa Biosystems). .. Cluster generation and sequencing were performed in a single-read mode using a TruSeq SR Cluster kit v3-cBot-HS (Illumina) and TruSeq SBS kit v3-HS (Illumina) according to manufacturer’s protocols.

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: Library quantification was performed using the qPCR-based Library Quantification Kit (Kapa Biosystems) to evaluate the molar concentration to be used in the sequencing runs. .. Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing.

Article Title: Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge
Article Snippet: Libraries were quantified using fluorometry with Qubit 2.0 (Life Technologies) and real-time PCR, and diluted to final concentration of 9 pM. .. Diluted libraries were clustered using a cBot instrument (Illumina) with a TruSeq PE Cluster Kit v3 (Illumina) and sequenced using a HiSeq 2000 sequencer (Illumina) with TruSeq SBS Kit v3-HS (Illumina), read length 101 from each end.

Incubation:

Article Title: Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus
Article Snippet: The cultures were then collected and incubated in H2 O at 25°C for 4 h. The treatments were repeated in triplicate for each strain. .. Samples were sequenced in a 1×100 nt way on an Illumina Hiseq2500 instrument using the TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina).

Expressing:

Article Title: Choice of binding sites for CTCFL compared to CTCF is driven by chromatin and by sequence preference
Article Snippet: Sequencing was done on the HiSeq 2500 (Illumina Inc.) using TruSeq SBS Kit v3 – HS (Illumina) for 50 cycles. .. Raw and processed data have been deposited in the NCBI gene expression omnibus (GEO) under accession number GSE103199.

Genome Wide:

Article Title: Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus
Article Snippet: Samples were sequenced in a 1×100 nt way on an Illumina Hiseq2500 instrument using the TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina). .. The data from triple biological replicates were then analyzed using Cufflinks software and resulted in quantified genome-wide transcript levels of genes (expressed in fragments per kilobase of exon model per million mapped fragments – FPKM) .

Flow Cytometry:

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: .. Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing. .. The primary analysis software Real Time Analysis (RTA 1.13.48) was used according to manufacturer’s protocol to process image analysis, base calling and base quality scoring of the run and followed by generation of fastq sequence files by CASAVA (v1.8).

Article Title: Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge
Article Snippet: Mate-paired libraries for the SOLiD 4 system (Life Technologies, Carlsbad, CA) with inserts of ~2.5 kb were constructed from 5 μg of genomic DNA, and deposited on two quarters of a flow cell for each sample. .. Diluted libraries were clustered using a cBot instrument (Illumina) with a TruSeq PE Cluster Kit v3 (Illumina) and sequenced using a HiSeq 2000 sequencer (Illumina) with TruSeq SBS Kit v3-HS (Illumina), read length 101 from each end.

Ligation:

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: Ligation to specific Illumina indexed paired-end adapters was performed following an adapter:insert molar ratio of 40:1, followed by a post-ligation cleanup step with 0.8X SPRI cleanup combining the previous reaction to Agencourt AMPure XP reagent (Beckman Coulter) to remove unligated adapters. .. Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing.

Article Title: Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes
Article Snippet: The cDNA sample was fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing. .. Sequencing was performed on the Illumina HiSeq 2000 single end 100 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc., California, USA).

Generated:

Article Title: Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus
Article Snippet: Samples were sequenced in a 1×100 nt way on an Illumina Hiseq2500 instrument using the TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina). .. The clean reads were generated by removing adaptor sequences, tags with > 10% “N”, and low quality tags by FastQC ( http://www.bioinformatics.babraham.ac.uk ), and were mapped to the M. oryzae genome database (MG8) ( www.broadinstitute.org ) using Tophat software .

Article Title: Deciphering the Genetic Blueprint behind Holstein Milk Proteins and Production
Article Snippet: We generated pair-end reads using Illumina HiSeq2000. .. Paired-end sequencing was conducted with NICEM (National Instrumentation Center for Environmental Management, Seoul, Korea) using the Illumina HiSeq2000 platform with TruSeq SBS Kit v3-HS (Illumina).

Article Title: Natural Variation of Molecular and Morphological Gibberellin Responses 1Natural Variation of Molecular and Morphological Gibberellin Responses 1 [OPEN]
Article Snippet: .. After quality control using the 2100 Bioanalyzer, clusters were generated through amplification using the TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina) followed by sequencing on a Illumina HiSeq 2000 with the TruSeq SBS Kit v3-HS (Illumina). .. Sequencing was performed in paired-end mode with a read length of 50 bp.

DNA Sequencing:

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: Paragraph title: 2.5. DNA-seq library preparation ... Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing.

Sequencing:

Article Title: Genomic Analysis Reveals Distinct Concentration-Dependent Evolutionary Trajectories for Antibiotic Resistance in Escherichia coli
Article Snippet: .. Sequencing and determination of mutations Library preparation was carried out using the Truseq DNA library sample prep kit V2, and sequencing was carried out using TruSeq SBS Kit v3-HS (50 Cycles) at Centre for Cellular and Molecular Platforms (C-CAMP) on Illumina HiSeq 1000 platform according to manufacturer's instructions. ..

Article Title: RNA-Seq Analysis Reveals Candidate Genes for Ontogenic Resistance in Malus-Venturia Pathosystem
Article Snippet: .. Sequencing was performed on the Illumina HiSeq 2000 paired-end at 2×101 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc.). .. RNA-seq reads were quality-checked with fastqc which computes various quality metrics for the raw reads.

Article Title: Deciphering the Genetic Blueprint behind Holstein Milk Proteins and Production
Article Snippet: .. Paired-end sequencing was conducted with NICEM (National Instrumentation Center for Environmental Management, Seoul, Korea) using the Illumina HiSeq2000 platform with TruSeq SBS Kit v3-HS (Illumina). .. Finally, sequence data were generated using the Illumina HiSeq system.

Article Title: Role of UHRF1 in de novo DNA methylation in oocytes and maintenance methylation in preimplantation embryos
Article Snippet: .. Cluster generation and sequencing were performed in a single-read mode using a TruSeq SR Cluster kit v3-cBot-HS (Illumina) and TruSeq SBS kit v3-HS (Illumina) according to manufacturer’s protocols. ..

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: Library quantification was performed using the qPCR-based Library Quantification Kit (Kapa Biosystems) to evaluate the molar concentration to be used in the sequencing runs. .. Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing.

Article Title: Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge
Article Snippet: Paragraph title: Genome sequencing ... Diluted libraries were clustered using a cBot instrument (Illumina) with a TruSeq PE Cluster Kit v3 (Illumina) and sequenced using a HiSeq 2000 sequencer (Illumina) with TruSeq SBS Kit v3-HS (Illumina), read length 101 from each end.

Article Title: Choice of binding sites for CTCFL compared to CTCF is driven by chromatin and by sequence preference
Article Snippet: .. Sequencing was done on the HiSeq 2500 (Illumina Inc.) using TruSeq SBS Kit v3 – HS (Illumina) for 50 cycles. ..

Article Title: Natural Variation of Molecular and Morphological Gibberellin Responses 1Natural Variation of Molecular and Morphological Gibberellin Responses 1 [OPEN]
Article Snippet: .. After quality control using the 2100 Bioanalyzer, clusters were generated through amplification using the TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina) followed by sequencing on a Illumina HiSeq 2000 with the TruSeq SBS Kit v3-HS (Illumina). .. Sequencing was performed in paired-end mode with a read length of 50 bp.

Article Title: Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions
Article Snippet: .. The libraries were sequenced using TruSeq SBS Kit v3-HS (Illumina Inc.), in paired end mode, 2x101bp, in ½ of a sequencing lane of HiSeq2000 flowcell v3 (Illumina Inc.) according to standard Illumina operation procedures with the yield of > 14Gb and median coverage of 33-41x. .. Primary data analysis, the image analysis, base calling and quality scoring of the run, was processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.

Article Title: Genomic analysis of fibrolamellar hepatocellular carcinoma
Article Snippet: .. Clustering was performed on the Illumina cBot using Illumina TruSeq PE Cluster kit v3, and sequencing was done on Illumina HiSeq 2000 using the Illumina TruSeq SBS Kit v3-HS to generate 2 × 100 pair end reads. ..

Article Title: Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum
Article Snippet: .. Sequencing was done on the HiSeq 2500 (Illumina, San Diego, CA, USA) using TruSeq SBS Kit v3 – HS (Illumina, San Diego, CA, USA) for 50 cycles. ..

Article Title: Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation
Article Snippet: .. Sequencing were performed on the Illumina HiSeq 2500 single-end at 1 × 100 bp using the TruSeq SBS Kit v3-HS (Illumina). .. RNA-sequencing read processing Illumina genome analyser pipeline software CASAVA (v. 1.8.2) was used for image analysis, base calling and FASTQ file generation.

Article Title: Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes
Article Snippet: .. Sequencing was performed on the Illumina HiSeq 2000 single end 100 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc., California, USA). ..

Article Title: Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters
Article Snippet: Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina, #FC-131- 1024) with approximately 480 pg of cDNA in a 4 μl tagmentation reaction followed by a dual indexing PCR with 9 cycles. .. The library pool was sequenced on a HiSeq 2500 (Illumina) using the TruSeq SBS Kit v3-HS (Illumina, #FC-401- 3001) in a single read run with 90 bp read length.

Sonication:

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: Physical fragmentation of DNA used the Covaris® instrument (Woburn, MA) as a sonication device using the Adaptive Focused Acoustics™ (AFA) technology. .. Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing.

Multiplexing:

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: .. Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing. .. The primary analysis software Real Time Analysis (RTA 1.13.48) was used according to manufacturer’s protocol to process image analysis, base calling and base quality scoring of the run and followed by generation of fastq sequence files by CASAVA (v1.8).

Article Title: Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes
Article Snippet: The cDNA sample was fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing. .. Sequencing was performed on the Illumina HiSeq 2000 single end 100 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc., California, USA).

RNA Sequencing Assay:

Article Title: RNA-Seq Analysis Reveals Candidate Genes for Ontogenic Resistance in Malus-Venturia Pathosystem
Article Snippet: Paragraph title: Sequencing and processing of RNA-Seq data ... Sequencing was performed on the Illumina HiSeq 2000 paired-end at 2×101 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc.).

Article Title: Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus
Article Snippet: Paragraph title: RNA-sequencing analysis ... Samples were sequenced in a 1×100 nt way on an Illumina Hiseq2500 instrument using the TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina).

Article Title: Natural Variation of Molecular and Morphological Gibberellin Responses 1Natural Variation of Molecular and Morphological Gibberellin Responses 1 [OPEN]
Article Snippet: Paragraph title: RNA-Seq Analysis ... After quality control using the 2100 Bioanalyzer, clusters were generated through amplification using the TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina) followed by sequencing on a Illumina HiSeq 2000 with the TruSeq SBS Kit v3-HS (Illumina).

Article Title: Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum
Article Snippet: Paragraph title: RNA Sequencing and Data Analysis ... Sequencing was done on the HiSeq 2500 (Illumina, San Diego, CA, USA) using TruSeq SBS Kit v3 – HS (Illumina, San Diego, CA, USA) for 50 cycles.

Article Title: Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes
Article Snippet: Paragraph title: RNA-sequencing and bioinformatic analysis ... Sequencing was performed on the Illumina HiSeq 2000 single end 100 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc., California, USA).

Article Title: Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters
Article Snippet: Paragraph title: Single-cell RNA-seq ... The library pool was sequenced on a HiSeq 2500 (Illumina) using the TruSeq SBS Kit v3-HS (Illumina, #FC-401- 3001) in a single read run with 90 bp read length.

Isolation:

Article Title: Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus
Article Snippet: Total RNA was extracted from ground mycelia in liquid nitrogen with the RNeasy Plant Mini Kit (QIAGEN), and mRNA was isolated using AMPure XP beads (Beckman). .. Samples were sequenced in a 1×100 nt way on an Illumina Hiseq2500 instrument using the TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina).

Article Title: Deciphering the Genetic Blueprint behind Holstein Milk Proteins and Production
Article Snippet: DNA was isolated from whole blood using a G-DEXTMIIb Genomic DNA Extraction Kit (iNtRoN Biotechnology, Seoul, Korea) according to the manufacturer’s protocol. .. Paired-end sequencing was conducted with NICEM (National Instrumentation Center for Environmental Management, Seoul, Korea) using the Illumina HiSeq2000 platform with TruSeq SBS Kit v3-HS (Illumina).

Purification:

Article Title: Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum
Article Snippet: Library purification was done using AMPure purification. .. Sequencing was done on the HiSeq 2500 (Illumina, San Diego, CA, USA) using TruSeq SBS Kit v3 – HS (Illumina, San Diego, CA, USA) for 50 cycles.

Article Title: Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters
Article Snippet: Individual single-cell libraries were pooled and purified with 0.8 × Agencourt Ampure XP Beads. .. The library pool was sequenced on a HiSeq 2500 (Illumina) using the TruSeq SBS Kit v3-HS (Illumina, #FC-401- 3001) in a single read run with 90 bp read length.

Polymerase Chain Reaction:

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: .. Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing. .. The primary analysis software Real Time Analysis (RTA 1.13.48) was used according to manufacturer’s protocol to process image analysis, base calling and base quality scoring of the run and followed by generation of fastq sequence files by CASAVA (v1.8).

Article Title: Genomic analysis of fibrolamellar hepatocellular carcinoma
Article Snippet: Clustering was performed on the Illumina cBot using Illumina TruSeq PE Cluster kit v3, and sequencing was done on Illumina HiSeq 2000 using the Illumina TruSeq SBS Kit v3-HS to generate 2 × 100 pair end reads. .. PCR duplicates were removed by Picard (picard.sourceforge.net).

Article Title: Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum
Article Snippet: The resulting di-tagged cDNA was amplified by PCR using primers that anneal to the two different tagging sequences on the cDNA to generate the library. .. Sequencing was done on the HiSeq 2500 (Illumina, San Diego, CA, USA) using TruSeq SBS Kit v3 – HS (Illumina, San Diego, CA, USA) for 50 cycles.

Article Title: Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes
Article Snippet: Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. .. Sequencing was performed on the Illumina HiSeq 2000 single end 100 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc., California, USA).

Article Title: Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters
Article Snippet: Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina, #FC-131- 1024) with approximately 480 pg of cDNA in a 4 μl tagmentation reaction followed by a dual indexing PCR with 9 cycles. .. The library pool was sequenced on a HiSeq 2500 (Illumina) using the TruSeq SBS Kit v3-HS (Illumina, #FC-401- 3001) in a single read run with 90 bp read length.

Chromatin Immunoprecipitation:

Article Title: Choice of binding sites for CTCFL compared to CTCF is driven by chromatin and by sequence preference
Article Snippet: Paragraph title: Deep sequencing of ChIP DNA and bioinformatics analysis ... Sequencing was done on the HiSeq 2500 (Illumina Inc.) using TruSeq SBS Kit v3 – HS (Illumina) for 50 cycles.

Software:

Article Title: Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus
Article Snippet: Samples were sequenced in a 1×100 nt way on an Illumina Hiseq2500 instrument using the TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina). .. The clean reads were generated by removing adaptor sequences, tags with > 10% “N”, and low quality tags by FastQC ( http://www.bioinformatics.babraham.ac.uk ), and were mapped to the M. oryzae genome database (MG8) ( www.broadinstitute.org ) using Tophat software .

Article Title: Deciphering the Genetic Blueprint behind Holstein Milk Proteins and Production
Article Snippet: Paired-end sequencing was conducted with NICEM (National Instrumentation Center for Environmental Management, Seoul, Korea) using the Illumina HiSeq2000 platform with TruSeq SBS Kit v3-HS (Illumina). .. We performed a per-base sequence quality check using the fastQC software ( http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ , last accessed October 28, 2013).

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing. .. The primary analysis software Real Time Analysis (RTA 1.13.48) was used according to manufacturer’s protocol to process image analysis, base calling and base quality scoring of the run and followed by generation of fastq sequence files by CASAVA (v1.8).

Article Title: Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions
Article Snippet: The libraries were sequenced using TruSeq SBS Kit v3-HS (Illumina Inc.), in paired end mode, 2x101bp, in ½ of a sequencing lane of HiSeq2000 flowcell v3 (Illumina Inc.) according to standard Illumina operation procedures with the yield of > 14Gb and median coverage of 33-41x. .. Primary data analysis, the image analysis, base calling and quality scoring of the run, was processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.

Functional Assay:

Article Title: Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes
Article Snippet: Transcriptome library preparation was performed at the Functional Genomics Center Zurich (FGCZ) using the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., California, USA) following the manufacturers’ protocols. .. Sequencing was performed on the Illumina HiSeq 2000 single end 100 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc., California, USA).

Selection:

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: The AMPure XP beads were also used for gDNA library size selection of 220–550 bp inserts. .. Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing.

Sample Prep:

Article Title: Genomic Analysis Reveals Distinct Concentration-Dependent Evolutionary Trajectories for Antibiotic Resistance in Escherichia coli
Article Snippet: .. Sequencing and determination of mutations Library preparation was carried out using the Truseq DNA library sample prep kit V2, and sequencing was carried out using TruSeq SBS Kit v3-HS (50 Cycles) at Centre for Cellular and Molecular Platforms (C-CAMP) on Illumina HiSeq 1000 platform according to manufacturer's instructions. ..

Article Title: Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus
Article Snippet: RNA-seq libraries were constructed using NEBNext RNA sample preparation kit (NEB) in accordance with the standard low-throughput protocol. .. Samples were sequenced in a 1×100 nt way on an Illumina Hiseq2500 instrument using the TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina).

Article Title: Deciphering the Genetic Blueprint behind Holstein Milk Proteins and Production
Article Snippet: The fragments of sheared DNA were end-repaired, A-tailed, adaptor ligated, and amplified using a TruSeq DNA Sample Prep. .. Paired-end sequencing was conducted with NICEM (National Instrumentation Center for Environmental Management, Seoul, Korea) using the Illumina HiSeq2000 platform with TruSeq SBS Kit v3-HS (Illumina).

Article Title: Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge
Article Snippet: To construct the libraries for whole-genome sequencing, DNA was processed using a TruSeq DNA Sample Preparation kit v.2 (Illumina, San Diego, CA) according to the manufacturer’s instructions. .. Diluted libraries were clustered using a cBot instrument (Illumina) with a TruSeq PE Cluster Kit v3 (Illumina) and sequenced using a HiSeq 2000 sequencer (Illumina) with TruSeq SBS Kit v3-HS (Illumina), read length 101 from each end.

Article Title: Natural Variation of Molecular and Morphological Gibberellin Responses 1Natural Variation of Molecular and Morphological Gibberellin Responses 1 [OPEN]
Article Snippet: Library preparation was done using the TruSeq RNA Sample Preparation Kit v2 (Illumina). .. After quality control using the 2100 Bioanalyzer, clusters were generated through amplification using the TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina) followed by sequencing on a Illumina HiSeq 2000 with the TruSeq SBS Kit v3-HS (Illumina).

Article Title: Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions
Article Snippet: TruSeq™DNA Sample Preparation Kit v2 (Illumina Inc.) and the KAPA Library Preparation kit (Kapa Biosystems) were used. .. The libraries were sequenced using TruSeq SBS Kit v3-HS (Illumina Inc.), in paired end mode, 2x101bp, in ½ of a sequencing lane of HiSeq2000 flowcell v3 (Illumina Inc.) according to standard Illumina operation procedures with the yield of > 14Gb and median coverage of 33-41x.

Article Title: Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes
Article Snippet: Transcriptome library preparation was performed at the Functional Genomics Center Zurich (FGCZ) using the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., California, USA) following the manufacturers’ protocols. .. Sequencing was performed on the Illumina HiSeq 2000 single end 100 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc., California, USA).

Article Title: Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters
Article Snippet: Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina, #FC-131- 1024) with approximately 480 pg of cDNA in a 4 μl tagmentation reaction followed by a dual indexing PCR with 9 cycles. .. The library pool was sequenced on a HiSeq 2500 (Illumina) using the TruSeq SBS Kit v3-HS (Illumina, #FC-401- 3001) in a single read run with 90 bp read length.

Concentration Assay:

Article Title: Comparative Genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity
Article Snippet: Library quantification was performed using the qPCR-based Library Quantification Kit (Kapa Biosystems) to evaluate the molar concentration to be used in the sequencing runs. .. Libraries were sequenced using the TruSeq SBS Kit v3-HS (Illumina Inc.), compatible with both PCR-free and PCR-amplified libraries, with a standard protocol ensuring a paired-end run of 2 ×101-bp long reads on a HiSeq 2000 flow cell v3 (Illumina Inc.) based on sample multiplexing.

Article Title: Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge
Article Snippet: Libraries were quantified using fluorometry with Qubit 2.0 (Life Technologies) and real-time PCR, and diluted to final concentration of 9 pM. .. Diluted libraries were clustered using a cBot instrument (Illumina) with a TruSeq PE Cluster Kit v3 (Illumina) and sequenced using a HiSeq 2000 sequencer (Illumina) with TruSeq SBS Kit v3-HS (Illumina), read length 101 from each end.

DNA Purification:

Article Title: Choice of binding sites for CTCFL compared to CTCF is driven by chromatin and by sequence preference
Article Snippet: Deep sequencing of ChIP DNA and bioinformatics analysis Samples were prepared as described for ChIP, but the elution step after DNA purification was performed with H2 O instead of elution buffer. .. Sequencing was done on the HiSeq 2500 (Illumina Inc.) using TruSeq SBS Kit v3 – HS (Illumina) for 50 cycles.

Lysis:

Article Title: Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters
Article Snippet: After cell lysis polyadenylated mRNA was reverse transcribed using a biotinylated template switch oligo (5′-Biotin-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′) with two riboguanosines (rG) and one LNA-modified guanosine (+G) at the 3′ end. .. The library pool was sequenced on a HiSeq 2500 (Illumina) using the TruSeq SBS Kit v3-HS (Illumina, #FC-401- 3001) in a single read run with 90 bp read length.

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  • 78
    Illumina Inc standard illumina kit reagents
    TAg mRNA abundance is high relative to RacPyV VP gene and to total gene transcription in tumors. Total RNA was extracted and filtered for polyadenylated RNA from two RacPyV PCR-positive tumor samples (Rac 10 and Rac 12) and two RacPyV PCR-negative-control olfactory bulbs. RNA was sequenced on an <t>Illumina</t> HiSeq 2000, and pooled quality reads were de novo assembled to produce a transcriptome that identified 13,473 protein-coding genes. Transcripts were quantified using RSEM, and genes from the tumor samples were plotted in order of decreasing TPM. Asterisks and inverted triangles indicate RacPyV TAg and VP genes, respectively.
    Standard Illumina Kit Reagents, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 78/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/standard illumina kit reagents/product/Illumina Inc
    Average 78 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    standard illumina kit reagents - by Bioz Stars, 2020-02
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    89
    Illumina Inc messenger rna sequencing
    Transcriptional modulation of select antimicrobial peptide genes in 3-dimensional endocervical aggregates. Differences in messenger <t>RNA</t> expression for 3 human β defensins (HBD-1, HBD-2, and HBD-4) and the secreted leukocyte peptidase inhibitor
    Messenger Rna Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/messenger rna sequencing/product/Illumina Inc
    Average 89 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    messenger rna sequencing - by Bioz Stars, 2020-02
    89/100 stars
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    99
    Illumina Inc truseq sbs kit v3 hs
    Transcriptional modulation of select antimicrobial peptide genes in 3-dimensional endocervical aggregates. Differences in messenger <t>RNA</t> expression for 3 human β defensins (HBD-1, HBD-2, and HBD-4) and the secreted leukocyte peptidase inhibitor
    Truseq Sbs Kit V3 Hs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 82 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq sbs kit v3 hs/product/Illumina Inc
    Average 99 stars, based on 82 article reviews
    Price from $9.99 to $1999.99
    truseq sbs kit v3 hs - by Bioz Stars, 2020-02
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    99
    Illumina Inc illumina hiseq 2000
    Transcriptional modulation of select antimicrobial peptide genes in 3-dimensional endocervical aggregates. Differences in messenger <t>RNA</t> expression for 3 human β defensins (HBD-1, HBD-2, and HBD-4) and the secreted leukocyte peptidase inhibitor
    Illumina Hiseq 2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 5538 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq 2000/product/Illumina Inc
    Average 99 stars, based on 5538 article reviews
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    illumina hiseq 2000 - by Bioz Stars, 2020-02
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    Image Search Results


    TAg mRNA abundance is high relative to RacPyV VP gene and to total gene transcription in tumors. Total RNA was extracted and filtered for polyadenylated RNA from two RacPyV PCR-positive tumor samples (Rac 10 and Rac 12) and two RacPyV PCR-negative-control olfactory bulbs. RNA was sequenced on an Illumina HiSeq 2000, and pooled quality reads were de novo assembled to produce a transcriptome that identified 13,473 protein-coding genes. Transcripts were quantified using RSEM, and genes from the tumor samples were plotted in order of decreasing TPM. Asterisks and inverted triangles indicate RacPyV TAg and VP genes, respectively.

    Journal: Journal of Virology

    Article Title: The Raccoon Polyomavirus Genome and Tumor Antigen Transcription Are Stable and Abundant in Neuroglial Tumors

    doi: 10.1128/JVI.01912-14

    Figure Lengend Snippet: TAg mRNA abundance is high relative to RacPyV VP gene and to total gene transcription in tumors. Total RNA was extracted and filtered for polyadenylated RNA from two RacPyV PCR-positive tumor samples (Rac 10 and Rac 12) and two RacPyV PCR-negative-control olfactory bulbs. RNA was sequenced on an Illumina HiSeq 2000, and pooled quality reads were de novo assembled to produce a transcriptome that identified 13,473 protein-coding genes. Transcripts were quantified using RSEM, and genes from the tumor samples were plotted in order of decreasing TPM. Asterisks and inverted triangles indicate RacPyV TAg and VP genes, respectively.

    Article Snippet: Indexed libraries were pooled and loaded on the cBot for cluster generation on TruSeq paired-end flow cells, and paired-end sequencing (2 × 100 bp, paired-end; 4 libraries/lane) was performed with an Illumina HiSeq 2000 sequencing system (BGI@UC Davis Joint Genome Center) using standard Illumina kit reagents (TruSeq SBS kit v3-HS).

    Techniques: Polymerase Chain Reaction, Negative Control

    Transcriptional modulation of select antimicrobial peptide genes in 3-dimensional endocervical aggregates. Differences in messenger RNA expression for 3 human β defensins (HBD-1, HBD-2, and HBD-4) and the secreted leukocyte peptidase inhibitor

    Journal: The Journal of Infectious Diseases

    Article Title: Mycoplasmagenitalium Infection Activates Cellular Host Defense and Inflammation Pathways in a 3-Dimensional Human Endocervical Epithelial Cell Model

    doi: 10.1093/infdis/jit101

    Figure Lengend Snippet: Transcriptional modulation of select antimicrobial peptide genes in 3-dimensional endocervical aggregates. Differences in messenger RNA expression for 3 human β defensins (HBD-1, HBD-2, and HBD-4) and the secreted leukocyte peptidase inhibitor

    Article Snippet: Equal 1-μg quantities of RNA were pooled from each experiment and used for library preparation (truSeq RNA Sample Prep Kit v2), cluster generation (TruSeq Single Read Cluster generation Kit v3-cBot-HS), and messenger RNA sequencing (mRNA-Seq; TruSeq SBS Kit v3-HS) on the Illumina HiSeq 2000 (Illumina, San Diego, CA). mRNA-Seq was conducted by SeqWright according to the manufacturer's protocol.

    Techniques: RNA Expression