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Illumina Inc hiseq 2500 sequencer
Hiseq 2500 Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 497 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/hiseq 2500 sequencer/product/Illumina Inc
Average 99 stars, based on 497 article reviews
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hiseq 2500 sequencer - by Bioz Stars, 2020-02
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Amplification:

Article Title: Genetic aberrations in iPSCs are introduced by a transient G1/S cell cycle checkpoint deficiency
Article Snippet: Ultra-deep VAF analysis The genomic region containing the target SNV site was amplified by PCR in a reaction containing 15 ng of genomic DNA prepared from iPSCs (2500 cells). .. PCR was performed using Titanium-taq DNA polymerase (Clontech, Palo Alto, CA) under the following conditions: 95 °C for 1 min followed by 32 cycles at 95 °C for 20 s, 68 °C for 30 s, and 72 °C for 30 s. The PCR products were mixed and purified using a MinElute PCR Purification Kit (Qiagen), and then subjected to comprehensive sequencing using a HiSeq 2500 sequencer (101 bp, paired-end, Illumina).

Article Title: Study on the Effect of Capsaicin on the Intestinal Flora through High-Throughput Sequencing
Article Snippet: The Vazyme Universal DNA Library Prep Kit for ILLUMINAV2 was used to prepare libraries of the PCR amplification products for next-generation sequencing. .. The paired-end 250-bp mode of an Illumina HiSeq 2500 sequencer was used.

Article Title: Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development
Article Snippet: Briefly, SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech, 643890) was used for reverse transcription and cDNA amplification (11 cycles). cDNA were then fragmented, adaptor-ligated and amplified using Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. .. Single-end 100-bp sequencing was performed on a HiSeq 2500 sequencer (Illumina).

Construct:

Article Title: Avian Intestinal Mucus Modulates Campylobacter jejuni Gene Expression in a Host-Specific Manner
Article Snippet: .. Libraries were constructed using directional TruSeq RNA library kit and were sequenced on a HiSeq 2500 sequencer using the 100-cycle, high output mode (Illumina Inc., San Diego, CA). .. Messenger RNA used for RNA-Seq analysis from C. jejuni grown on chicken mucus was sequenced using PacBio's long read technology to evaluate if antisense RNA resulted from pervasive transcription extending from adjacent upregulated mRNA.

Real-time Polymerase Chain Reaction:

Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
Article Snippet: The prepared libraries were quantified using the Kapa Biosystems next-generation sequencing library quantitative PCR (qPCR) kit and run on a Roche LightCycler 480 real-time PCR instrument. .. Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe ( ).

Incubation:

Article Title: Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development
Article Snippet: Specifically, the embryos were briefly incubated in Acid Tyrode (Millipore) to remove zona pellucida and then washed three times in 0.2% BSA/PBS prior for library construction. .. Single-end 100-bp sequencing was performed on a HiSeq 2500 sequencer (Illumina).

In Silico:

Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
Article Snippet: Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe ( ). .. For CBS463.89 lacking LMP, the initial assemblies of fragment data with Velvet v.1.2.07 ( ) were used to create in silico long mate pair libraries with insert sizes of 3,000 ± 300 bp.

Western Blot:

Article Title: Expanding the global prevalence of spinocerebellar ataxia type 42
Article Snippet: Sequencing for these libraries was performed with 107-bp paired-end reads on a HiSeq 2500 sequencer in the rapid-run mode platform (Illumina, San Diego, CA). .. Linkage analysis was conducted with ALLEGRO on 190,569 single nucleotide polymorphisms (SNPs) (average distance between SNPs ≈ 0.015 Mb) under a dominant model (f0 /f1 /f2 = 0/1/1) with estimated minor allele frequencies drawn from HapMap3 project Centre d'Etude du Polymorphism Humain - Utah population data, comprised Utah residents with Northern and Western European ancestry.

Flow Cytometry:

Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
Article Snippet: .. Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe ( ). .. Illumina FASTQ files were quality control (QC) filtered for artifact/process contamination.

Article Title: Genomic sequence data and single nucleotide polymorphism genotyping of Bacillus anthracis strains isolated from animal anthrax outbreaks in Northern Cape Province, South Africa
Article Snippet: Clusters were generated on the flow cell using HiSeq Paired-End Cluster Generation kit (Ilumina, USA) for the HiSeq 2500 platform. .. Sequencing of paired end libraries were performed on the Illumina MiSeq and HiSeq 2500 sequencer using the 200-cycle SBS (sequencing by synthesis) sequencing v3 kit (Illumina, USA) and HiSeq Sequencing Kit (200 cycles) (Illumina, USA) respectively.

Ligation:

Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
Article Snippet: For the transcriptomes, which were used for genome annotations, stranded cDNA libraries were generated using the Illumina TruSeq stranded RNA low-throughput (LT) kit. mRNA was purified using magnetic beads containing poly(T) oligonucleotides, fragmented and reverse transcribed using random hexamers and SSII (Invitrogen), followed by second-strand synthesis, and then treated with end repair, A-tailing, adapter ligation, and eight PCR cycles. .. Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe ( ).

Article Title: Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer
Article Snippet: A single A base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). .. Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

Methylation:

Article Title: SMaSH: Sample matching using SNPs in humans
Article Snippet: Libraries with compatible barcodes were pooled and sequenced on Illumina HiSeq 2500 Sequencer using High Output Mode to achieve 35 to 40 million passed filtered single-end 50bp reads per sample. .. MethylCap-Seq libraries were prepared by enriching methylated DNA fragments (150-200 bp) using the methyl binding domain (MBD) of human MeCP2 (Auto MethylCap Kit, Diagenode, Denville, NJ) on the Diagenode SX-8G IP-Star Automated System as described by the manufacturer’s protocol.

Northern Blot:

Article Title: Expanding the global prevalence of spinocerebellar ataxia type 42
Article Snippet: Sequencing for these libraries was performed with 107-bp paired-end reads on a HiSeq 2500 sequencer in the rapid-run mode platform (Illumina, San Diego, CA). .. Linkage analysis was conducted with ALLEGRO on 190,569 single nucleotide polymorphisms (SNPs) (average distance between SNPs ≈ 0.015 Mb) under a dominant model (f0 /f1 /f2 = 0/1/1) with estimated minor allele frequencies drawn from HapMap3 project Centre d'Etude du Polymorphism Humain - Utah population data, comprised Utah residents with Northern and Western European ancestry.

Generated:

Article Title: Unique primed status of microglia under the systemic autoimmune condition of lupus-prone mice
Article Snippet: RNA-seq libraries were generated with the Ovation SoLo RNA-Seq System, Mouse kit (NuGEN, Redwood City, CA, USA) using 5 ng of total RNA. .. The cDNA libraries were sequenced by 50-base single-read sequencing on an Illumina HiSeq 2500 sequencer (Illumina, San Diego, CA, USA).

Article Title: Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases
Article Snippet: .. Libraries were prepared using the Nextera XT DNA Library Prep Kit and run on the Illumina HiSeq 2500 sequencer that generated 2 x 125bp paired-end reads. ..

Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
Article Snippet: For the transcriptomes, which were used for genome annotations, stranded cDNA libraries were generated using the Illumina TruSeq stranded RNA low-throughput (LT) kit. mRNA was purified using magnetic beads containing poly(T) oligonucleotides, fragmented and reverse transcribed using random hexamers and SSII (Invitrogen), followed by second-strand synthesis, and then treated with end repair, A-tailing, adapter ligation, and eight PCR cycles. .. Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe ( ).

Article Title: SMaSH: Sample matching using SNPs in humans
Article Snippet: Data set 1 and 4 libraries were generated using the stranded total transcriptome Illumina kit (TruSeq Stranded Total RNA LT with Ribo-Zero Gold; RS-122-2301). .. Libraries with compatible barcodes were pooled and sequenced on Illumina HiSeq 2500 Sequencer using High Output Mode to achieve 35 to 40 million passed filtered paired-end 50bp reads per sample.

Article Title: SMaSH: Sample matching using SNPs in humans
Article Snippet: RNA-Seq libraries were generated using the non-stranded Illumina kit (TruSeq RNA Sample Prep Kit; RS-122-2001). .. Libraries with compatible barcodes were pooled and sequenced on Illumina HiSeq 2500 Sequencer using High Output Mode to achieve 35 to 40 million passed filtered single-end 50bp reads per sample.

Article Title: Genomic sequence data and single nucleotide polymorphism genotyping of Bacillus anthracis strains isolated from animal anthrax outbreaks in Northern Cape Province, South Africa
Article Snippet: Clusters were generated on the flow cell using HiSeq Paired-End Cluster Generation kit (Ilumina, USA) for the HiSeq 2500 platform. .. Sequencing of paired end libraries were performed on the Illumina MiSeq and HiSeq 2500 sequencer using the 200-cycle SBS (sequencing by synthesis) sequencing v3 kit (Illumina, USA) and HiSeq Sequencing Kit (200 cycles) (Illumina, USA) respectively.

DNA Sequencing:

Article Title: Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer
Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing ... Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

Transmission Assay:

Article Title: Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases
Article Snippet: Libraries were prepared using the Nextera XT DNA Library Prep Kit and run on the Illumina HiSeq 2500 sequencer that generated 2 x 125bp paired-end reads. .. The MHSs assessed whether transmission was likely between the 134 clustered patients using information they obtained during interviews with the patients over several months.

Sequencing:

Article Title: Avian Intestinal Mucus Modulates Campylobacter jejuni Gene Expression in a Host-Specific Manner
Article Snippet: Paragraph title: mRNA Isolation and Sequencing ... Libraries were constructed using directional TruSeq RNA library kit and were sequenced on a HiSeq 2500 sequencer using the 100-cycle, high output mode (Illumina Inc., San Diego, CA).

Article Title: Unique primed status of microglia under the systemic autoimmune condition of lupus-prone mice
Article Snippet: .. The cDNA libraries were sequenced by 50-base single-read sequencing on an Illumina HiSeq 2500 sequencer (Illumina, San Diego, CA, USA). .. The sequencing run and the base call analysis were performed according to the HiSeq 2500 System Guide with TruSeq SBS kit v3-HS.

Article Title: Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases
Article Snippet: Paragraph title: Whole genome sequencing dataset from the Netherlands ... Libraries were prepared using the Nextera XT DNA Library Prep Kit and run on the Illumina HiSeq 2500 sequencer that generated 2 x 125bp paired-end reads.

Article Title: Genetic aberrations in iPSCs are introduced by a transient G1/S cell cycle checkpoint deficiency
Article Snippet: .. PCR was performed using Titanium-taq DNA polymerase (Clontech, Palo Alto, CA) under the following conditions: 95 °C for 1 min followed by 32 cycles at 95 °C for 20 s, 68 °C for 30 s, and 72 °C for 30 s. The PCR products were mixed and purified using a MinElute PCR Purification Kit (Qiagen), and then subjected to comprehensive sequencing using a HiSeq 2500 sequencer (101 bp, paired-end, Illumina). ..

Article Title: Study on the Effect of Capsaicin on the Intestinal Flora through High-Throughput Sequencing
Article Snippet: The paired-end 250-bp mode of an Illumina HiSeq 2500 sequencer was used. .. Then, the sequencing results were analyzed using the QIIME2 software package.

Article Title: Deficiency of Dietary Fiber in Slc5a8-Null Mice Promotes Bacterial Dysbiosis and Alters Colonic Epithelial Transcriptome towards Proinflammatory Milieu
Article Snippet: .. The pooled denatured cDNA libraries were loaded on a cBot for cluster generation followed by 2 × 108 bp paired-end sequencing using HiSeq Rapid kits with V2 chemistry on an HiSeq 2500 sequencer (Illumina, San Diego, USA). .. All the sequence files were uploaded into the NCBI-Sequence Read Archive (SRA) and Bio project ID: PRJNA517543 and used for data analysis.

Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
Article Snippet: .. Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe ( ). .. Illumina FASTQ files were quality control (QC) filtered for artifact/process contamination.

Article Title: Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development
Article Snippet: .. Single-end 100-bp sequencing was performed on a HiSeq 2500 sequencer (Illumina). .. RNA-seq analyses RNA-seq reads were first trimmed to remove adaptor sequences and low-quality bases using Trimgalore (version 0.4.5).

Article Title: SMaSH: Sample matching using SNPs in humans
Article Snippet: The rest of this section describes the library preparation, sequencing, and alignment steps for the in house data sets. .. Libraries with compatible barcodes were pooled and sequenced on Illumina HiSeq 2500 Sequencer using High Output Mode to achieve 35 to 40 million passed filtered paired-end 50bp reads per sample.

Article Title: Expanding the global prevalence of spinocerebellar ataxia type 42
Article Snippet: .. Sequencing for these libraries was performed with 107-bp paired-end reads on a HiSeq 2500 sequencer in the rapid-run mode platform (Illumina, San Diego, CA). .. The gDNA library for B-III-3 was prepared using the SureSelect Human All Exon V4 Capture kit (Agilent Technologies, Santa Clara, CA), and 101-bp paired-end reads were sequenced on the Illumina HiSeq 4000 platform (Illumina, San Diego, CA).

Article Title: SMaSH: Sample matching using SNPs in humans
Article Snippet: Libraries with compatible barcodes were pooled and sequenced on Illumina HiSeq 2500 Sequencer using High Output Mode to achieve 35 to 40 million passed filtered single-end 50bp reads per sample. .. Illumina sequencing libraries were generated from the enriched methylated material as previously described [ ].

Article Title: Genomic sequence data and single nucleotide polymorphism genotyping of Bacillus anthracis strains isolated from animal anthrax outbreaks in Northern Cape Province, South Africa
Article Snippet: .. Sequencing of paired end libraries were performed on the Illumina MiSeq and HiSeq 2500 sequencer using the 200-cycle SBS (sequencing by synthesis) sequencing v3 kit (Illumina, USA) and HiSeq Sequencing Kit (200 cycles) (Illumina, USA) respectively. .. Quality of the genome sequenced reads were assessed using FastQC software 0:10.1 [ ].

Binding Assay:

Article Title: SMaSH: Sample matching using SNPs in humans
Article Snippet: Libraries with compatible barcodes were pooled and sequenced on Illumina HiSeq 2500 Sequencer using High Output Mode to achieve 35 to 40 million passed filtered single-end 50bp reads per sample. .. MethylCap-Seq libraries were prepared by enriching methylated DNA fragments (150-200 bp) using the methyl binding domain (MBD) of human MeCP2 (Auto MethylCap Kit, Diagenode, Denville, NJ) on the Diagenode SX-8G IP-Star Automated System as described by the manufacturer’s protocol.

DNA Extraction:

Article Title: Study on the Effect of Capsaicin on the Intestinal Flora through High-Throughput Sequencing
Article Snippet: Paragraph title: DNA Isolation, PCR, and 16S rRNA Gene Analysis ... The paired-end 250-bp mode of an Illumina HiSeq 2500 sequencer was used.

RNA Sequencing Assay:

Article Title: Unique primed status of microglia under the systemic autoimmune condition of lupus-prone mice
Article Snippet: Paragraph title: RNA-seq analysis ... The cDNA libraries were sequenced by 50-base single-read sequencing on an Illumina HiSeq 2500 sequencer (Illumina, San Diego, CA, USA).

Article Title: Deficiency of Dietary Fiber in Slc5a8-Null Mice Promotes Bacterial Dysbiosis and Alters Colonic Epithelial Transcriptome towards Proinflammatory Milieu
Article Snippet: Paragraph title: 2.7. Library Preparations and RNA Sequencing ... The pooled denatured cDNA libraries were loaded on a cBot for cluster generation followed by 2 × 108 bp paired-end sequencing using HiSeq Rapid kits with V2 chemistry on an HiSeq 2500 sequencer (Illumina, San Diego, USA).

Article Title: Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development
Article Snippet: Paragraph title: RNA-seq ... Single-end 100-bp sequencing was performed on a HiSeq 2500 sequencer (Illumina).

Article Title: SMaSH: Sample matching using SNPs in humans
Article Snippet: Family RNA-Seq data [ ] was obtained from the European Nucleotide Archive under accession numbers PRJEB5063 and PRJEB3030 (SAMEA1325278). .. Libraries with compatible barcodes were pooled and sequenced on Illumina HiSeq 2500 Sequencer using High Output Mode to achieve 35 to 40 million passed filtered paired-end 50bp reads per sample.

Article Title: SMaSH: Sample matching using SNPs in humans
Article Snippet: RNA-Seq libraries were generated using the non-stranded Illumina kit (TruSeq RNA Sample Prep Kit; RS-122-2001). .. Libraries with compatible barcodes were pooled and sequenced on Illumina HiSeq 2500 Sequencer using High Output Mode to achieve 35 to 40 million passed filtered single-end 50bp reads per sample.

Magnetic Beads:

Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
Article Snippet: For the transcriptomes, which were used for genome annotations, stranded cDNA libraries were generated using the Illumina TruSeq stranded RNA low-throughput (LT) kit. mRNA was purified using magnetic beads containing poly(T) oligonucleotides, fragmented and reverse transcribed using random hexamers and SSII (Invitrogen), followed by second-strand synthesis, and then treated with end repair, A-tailing, adapter ligation, and eight PCR cycles. .. Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe ( ).

Isolation:

Article Title: Avian Intestinal Mucus Modulates Campylobacter jejuni Gene Expression in a Host-Specific Manner
Article Snippet: Paragraph title: mRNA Isolation and Sequencing ... Libraries were constructed using directional TruSeq RNA library kit and were sequenced on a HiSeq 2500 sequencer using the 100-cycle, high output mode (Illumina Inc., San Diego, CA).

Article Title: Unique primed status of microglia under the systemic autoimmune condition of lupus-prone mice
Article Snippet: RNA-seq analysis Total RNA was isolated from sorted microglia using an RNeasy Micro Kit (Qiagen, Hilden, Germany) and further purified using NucleoSpin RNA XS (Takara Bio Inc., Kusatsu, Japan/Macherey-Nagel, Düren, Germany). .. The cDNA libraries were sequenced by 50-base single-read sequencing on an Illumina HiSeq 2500 sequencer (Illumina, San Diego, CA, USA).

Article Title: Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases
Article Snippet: DNA used for sequencing was isolated from positive Mycobacteria Growth Indicator Tubes and purified with the QIAamp DNA mini kit method (QIAGEN GmbH, Hilden, Germany). .. Libraries were prepared using the Nextera XT DNA Library Prep Kit and run on the Illumina HiSeq 2500 sequencer that generated 2 x 125bp paired-end reads.

Purification:

Article Title: Unique primed status of microglia under the systemic autoimmune condition of lupus-prone mice
Article Snippet: RNA-seq analysis Total RNA was isolated from sorted microglia using an RNeasy Micro Kit (Qiagen, Hilden, Germany) and further purified using NucleoSpin RNA XS (Takara Bio Inc., Kusatsu, Japan/Macherey-Nagel, Düren, Germany). .. The cDNA libraries were sequenced by 50-base single-read sequencing on an Illumina HiSeq 2500 sequencer (Illumina, San Diego, CA, USA).

Article Title: Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases
Article Snippet: DNA used for sequencing was isolated from positive Mycobacteria Growth Indicator Tubes and purified with the QIAamp DNA mini kit method (QIAGEN GmbH, Hilden, Germany). .. Libraries were prepared using the Nextera XT DNA Library Prep Kit and run on the Illumina HiSeq 2500 sequencer that generated 2 x 125bp paired-end reads.

Article Title: Genetic aberrations in iPSCs are introduced by a transient G1/S cell cycle checkpoint deficiency
Article Snippet: .. PCR was performed using Titanium-taq DNA polymerase (Clontech, Palo Alto, CA) under the following conditions: 95 °C for 1 min followed by 32 cycles at 95 °C for 20 s, 68 °C for 30 s, and 72 °C for 30 s. The PCR products were mixed and purified using a MinElute PCR Purification Kit (Qiagen), and then subjected to comprehensive sequencing using a HiSeq 2500 sequencer (101 bp, paired-end, Illumina). ..

Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
Article Snippet: For the transcriptomes, which were used for genome annotations, stranded cDNA libraries were generated using the Illumina TruSeq stranded RNA low-throughput (LT) kit. mRNA was purified using magnetic beads containing poly(T) oligonucleotides, fragmented and reverse transcribed using random hexamers and SSII (Invitrogen), followed by second-strand synthesis, and then treated with end repair, A-tailing, adapter ligation, and eight PCR cycles. .. Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe ( ).

Polymerase Chain Reaction:

Article Title: Genetic aberrations in iPSCs are introduced by a transient G1/S cell cycle checkpoint deficiency
Article Snippet: .. PCR was performed using Titanium-taq DNA polymerase (Clontech, Palo Alto, CA) under the following conditions: 95 °C for 1 min followed by 32 cycles at 95 °C for 20 s, 68 °C for 30 s, and 72 °C for 30 s. The PCR products were mixed and purified using a MinElute PCR Purification Kit (Qiagen), and then subjected to comprehensive sequencing using a HiSeq 2500 sequencer (101 bp, paired-end, Illumina). ..

Article Title: Study on the Effect of Capsaicin on the Intestinal Flora through High-Throughput Sequencing
Article Snippet: Paragraph title: DNA Isolation, PCR, and 16S rRNA Gene Analysis ... The paired-end 250-bp mode of an Illumina HiSeq 2500 sequencer was used.

Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
Article Snippet: For the transcriptomes, which were used for genome annotations, stranded cDNA libraries were generated using the Illumina TruSeq stranded RNA low-throughput (LT) kit. mRNA was purified using magnetic beads containing poly(T) oligonucleotides, fragmented and reverse transcribed using random hexamers and SSII (Invitrogen), followed by second-strand synthesis, and then treated with end repair, A-tailing, adapter ligation, and eight PCR cycles. .. Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe ( ).

Article Title: Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer
Article Snippet: PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). .. Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

cDNA Library Assay:

Article Title: Deficiency of Dietary Fiber in Slc5a8-Null Mice Promotes Bacterial Dysbiosis and Alters Colonic Epithelial Transcriptome towards Proinflammatory Milieu
Article Snippet: Library Preparations and RNA Sequencing Total RNA was used for the cDNA library construction using TruSeq® Stranded mRNA LT kit (Illumina, San Diego, USA) and epMotion 5075t robot (Eppendorf, Hamburg, Germany). .. The pooled denatured cDNA libraries were loaded on a cBot for cluster generation followed by 2 × 108 bp paired-end sequencing using HiSeq Rapid kits with V2 chemistry on an HiSeq 2500 sequencer (Illumina, San Diego, USA).

Chromatin Immunoprecipitation:

Article Title: Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer
Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing ... Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

Software:

Article Title: Study on the Effect of Capsaicin on the Intestinal Flora through High-Throughput Sequencing
Article Snippet: The paired-end 250-bp mode of an Illumina HiSeq 2500 sequencer was used. .. Then, the sequencing results were analyzed using the QIIME2 software package.

Article Title: Genomic sequence data and single nucleotide polymorphism genotyping of Bacillus anthracis strains isolated from animal anthrax outbreaks in Northern Cape Province, South Africa
Article Snippet: Sequencing of paired end libraries were performed on the Illumina MiSeq and HiSeq 2500 sequencer using the 200-cycle SBS (sequencing by synthesis) sequencing v3 kit (Illumina, USA) and HiSeq Sequencing Kit (200 cycles) (Illumina, USA) respectively. .. Quality of the genome sequenced reads were assessed using FastQC software 0:10.1 [ ].

RNA Extraction:

Article Title: Avian Intestinal Mucus Modulates Campylobacter jejuni Gene Expression in a Host-Specific Manner
Article Snippet: After a period of 24 h, the cultures were removed from the incubator and RNAprotect (QIAGEN, Germantown, MD) was added to each culture followed by RNA extraction using the RNeasy extraction kit (QIAGEN), following the manufacturer's instructions. .. Libraries were constructed using directional TruSeq RNA library kit and were sequenced on a HiSeq 2500 sequencer using the 100-cycle, high output mode (Illumina Inc., San Diego, CA).

Sample Prep:

Article Title: SMaSH: Sample matching using SNPs in humans
Article Snippet: Paragraph title: Sample preparation and alignment ... Libraries with compatible barcodes were pooled and sequenced on Illumina HiSeq 2500 Sequencer using High Output Mode to achieve 35 to 40 million passed filtered paired-end 50bp reads per sample.

Article Title: Genomic sequence data and single nucleotide polymorphism genotyping of Bacillus anthracis strains isolated from animal anthrax outbreaks in Northern Cape Province, South Africa
Article Snippet: 2.3 High-throughput sequencing and bioinformatics analysis The DNA samples that were extracted from B. anthracis were subjected to library preparation by using the Nextera XT DNA Sample Prep kit (Illumina-compatible, Epicentre Biotechnology). .. Sequencing of paired end libraries were performed on the Illumina MiSeq and HiSeq 2500 sequencer using the 200-cycle SBS (sequencing by synthesis) sequencing v3 kit (Illumina, USA) and HiSeq Sequencing Kit (200 cycles) (Illumina, USA) respectively.

Next-Generation Sequencing:

Article Title: Study on the Effect of Capsaicin on the Intestinal Flora through High-Throughput Sequencing
Article Snippet: The Vazyme Universal DNA Library Prep Kit for ILLUMINAV2 was used to prepare libraries of the PCR amplification products for next-generation sequencing. .. The paired-end 250-bp mode of an Illumina HiSeq 2500 sequencer was used.

Article Title: Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens
Article Snippet: The prepared libraries were quantified using the Kapa Biosystems next-generation sequencing library quantitative PCR (qPCR) kit and run on a Roche LightCycler 480 real-time PCR instrument. .. Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe ( ).

Produced:

Article Title: Deficiency of Dietary Fiber in Slc5a8-Null Mice Promotes Bacterial Dysbiosis and Alters Colonic Epithelial Transcriptome towards Proinflammatory Milieu
Article Snippet: Library construction produced single-indexed libraries with a median insert size of ∼300 bp which was validated on an Agilent 2200 TapeStation instrument using D1000 ScreenTapes (Santa Clara, CA, USA). .. The pooled denatured cDNA libraries were loaded on a cBot for cluster generation followed by 2 × 108 bp paired-end sequencing using HiSeq Rapid kits with V2 chemistry on an HiSeq 2500 sequencer (Illumina, San Diego, USA).

High Throughput Screening Assay:

Article Title: Genomic sequence data and single nucleotide polymorphism genotyping of Bacillus anthracis strains isolated from animal anthrax outbreaks in Northern Cape Province, South Africa
Article Snippet: Paragraph title: High-throughput sequencing and bioinformatics analysis ... Sequencing of paired end libraries were performed on the Illumina MiSeq and HiSeq 2500 sequencer using the 200-cycle SBS (sequencing by synthesis) sequencing v3 kit (Illumina, USA) and HiSeq Sequencing Kit (200 cycles) (Illumina, USA) respectively.

Gel Extraction:

Article Title: Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer
Article Snippet: PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). .. Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

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    Illumina Inc hiseq 2500 platform
    Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina <t>HiSeq</t> 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.
    Hiseq 2500 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 690 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 2500 platform/product/Illumina Inc
    Average 99 stars, based on 690 article reviews
    Price from $9.99 to $1999.99
    hiseq 2500 platform - by Bioz Stars, 2020-02
    99/100 stars
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    Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization

    doi: 10.1073/pnas.1613294113

    Figure Lengend Snippet: Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.

    Article Snippet: The MALBAC single-cell WGA method was used to amplify DNA from the culture medium, as well as from the embryos, following the manufacturer’s protocol (catalog no. YK001B; Yikon Genomics), and used to construct the sequencing libraries (NEBNext Ultra DNA Kit; New England Biolabs) for sequencing on an Illumina HiSeq 2500 platform, yielding ∼2 million sequencing reads on each sample.

    Techniques: Injection, Whole Genome Amplification, Multiple Annealing and Looping–Based Amplification Cycles, Amplification

    Experimental scheme. ( A ) After differentiation, the cell cultures were dissociated to single-cell suspensions and loaded onto a Fluidigm C1 Single-Cell Auto Prep Array for mRNA-Seq. On the arrays, the cells were lysed, and reverse transcription of the mRNA and PCR amplification of the cDNA were performed using the C1 Single-Cell Auto Prep System (Fluidigm). Libraries were then prepared using the Nextera XT DNA Library Prep Kit and mosquito HTS liquid handler (TTP). For the final PCR reactions, we used a Bio-Rad 384 Thermal Cycler. Libraries were pooled and sequenced on an Illumina HiSeq 2500. ( B ) WA09 human embryonic stem cells were differentiated in vitro to the pancreatic lineage. Cells from stages 1 and 2 were collected and analyzed using the procedures outlined in A . Two independent cells from stage 1 (cell A and cell B) and two cells from stage 2 (cell C and cell D) were selected and yielded with similar cDNA concentrations (mean [SD] concentration = 0.38 [0.04] ng/µL). For library preparation, we tested 2-µL, 4-µL, and 8-µL final volume reactions, with four replicates per reaction volume.

    Journal: Jala (Charlottesville, Va.)

    Article Title: Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing

    doi: 10.1177/2211068216630741

    Figure Lengend Snippet: Experimental scheme. ( A ) After differentiation, the cell cultures were dissociated to single-cell suspensions and loaded onto a Fluidigm C1 Single-Cell Auto Prep Array for mRNA-Seq. On the arrays, the cells were lysed, and reverse transcription of the mRNA and PCR amplification of the cDNA were performed using the C1 Single-Cell Auto Prep System (Fluidigm). Libraries were then prepared using the Nextera XT DNA Library Prep Kit and mosquito HTS liquid handler (TTP). For the final PCR reactions, we used a Bio-Rad 384 Thermal Cycler. Libraries were pooled and sequenced on an Illumina HiSeq 2500. ( B ) WA09 human embryonic stem cells were differentiated in vitro to the pancreatic lineage. Cells from stages 1 and 2 were collected and analyzed using the procedures outlined in A . Two independent cells from stage 1 (cell A and cell B) and two cells from stage 2 (cell C and cell D) were selected and yielded with similar cDNA concentrations (mean [SD] concentration = 0.38 [0.04] ng/µL). For library preparation, we tested 2-µL, 4-µL, and 8-µL final volume reactions, with four replicates per reaction volume.

    Article Snippet: Sequencing The 48 pooled libraries were sequenced on one lane of an Illumina HiSeq 2500 at an average total read depth of 5.6 million reads per sample (ST3).

    Techniques: Polymerase Chain Reaction, Amplification, In Vitro, Concentration Assay

    Illustrated representation of the optimized barcoded cDNA library preparation procedure. Total RNA from formalin-fixed paraffin-embedded (FFPE) specimens ( n = 18), are ligated with 3′ adapters ( n = 18), purified on a 15% PAGE gel (using size markers (SM) RNA oligonucleotides) and excised after SYBR ® gold staining of the gel. The combined purified products are ligated with a 5′ adapter, run on a 12% PAGE gel, excised and purified. The dual-adapter ligated small-RNA products are reverse transcribed, subjected to a pilot PCR for identification of adequate amplification cycle. A large-scale PCR is performed, and the products are separated on a 2% agarose gel, where the upper band (cDNA library) is purified and subjected to sequencing on an Illumina HiSeq-2500 sequencer.

    Journal: International Journal of Molecular Sciences

    Article Title: Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens

    doi: 10.3390/ijms18030627

    Figure Lengend Snippet: Illustrated representation of the optimized barcoded cDNA library preparation procedure. Total RNA from formalin-fixed paraffin-embedded (FFPE) specimens ( n = 18), are ligated with 3′ adapters ( n = 18), purified on a 15% PAGE gel (using size markers (SM) RNA oligonucleotides) and excised after SYBR ® gold staining of the gel. The combined purified products are ligated with a 5′ adapter, run on a 12% PAGE gel, excised and purified. The dual-adapter ligated small-RNA products are reverse transcribed, subjected to a pilot PCR for identification of adequate amplification cycle. A large-scale PCR is performed, and the products are separated on a 2% agarose gel, where the upper band (cDNA library) is purified and subjected to sequencing on an Illumina HiSeq-2500 sequencer.

    Article Snippet: As there were no matched fresh or frozen total RNA for these samples, we duplicated our measures (200, 100 and 50 ng for all three tissues) to evaluate reproducibility and analyzed the resulting 18 RNA samples (with 18 unique 3′ barcoded adapters) in a single sequencing lane on an Illumina HiSeq 2500.

    Techniques: cDNA Library Assay, Formalin-fixed Paraffin-Embedded, Purification, Polyacrylamide Gel Electrophoresis, Staining, Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Sequencing

    VGSC small RNAs persist until the adult stage of  Ae. aegypti  treated by dsRNA-VGSC during larval stage.  a  Small RNA libraries were constructed from 5 day-old adult mosquitoes previously soaked in VGSC 422  dsRNA or Random dsRNA (0.5 μg/μl) and sequenced using Hiseq 2500. Data are presented as the number of reads normalized to one million mapped reads per sample (RPM). Forward strand (sense) reads are positive RPM values (depicted in  blue ); reverse strand (anti-sense) reads are in negative RPM values (depicted in  red ). Positions for which RPM values are  >  = 10 RPM were considered expressed.  b  Size distribution of small RNAs matching the VGSC422 transcript (Accession no. KC107440.1). nt: nucleotides

    Journal: Parasites & Vectors

    Article Title: Larval application of sodium channel homologous dsRNA restores pyrethroid insecticide susceptibility in a resistant adult mosquito population

    doi: 10.1186/s13071-016-1634-y

    Figure Lengend Snippet: VGSC small RNAs persist until the adult stage of Ae. aegypti treated by dsRNA-VGSC during larval stage. a Small RNA libraries were constructed from 5 day-old adult mosquitoes previously soaked in VGSC 422 dsRNA or Random dsRNA (0.5 μg/μl) and sequenced using Hiseq 2500. Data are presented as the number of reads normalized to one million mapped reads per sample (RPM). Forward strand (sense) reads are positive RPM values (depicted in blue ); reverse strand (anti-sense) reads are in negative RPM values (depicted in red ). Positions for which RPM values are  >  = 10 RPM were considered expressed. b Size distribution of small RNAs matching the VGSC422 transcript (Accession no. KC107440.1). nt: nucleotides

    Article Snippet: Sequencing was performed in a Hiseq 2500 (Illumina, USA) instrument, in a 100 bp single-end read run using HiSeq SBS clustering and sequencing kit v3-HS.

    Techniques: Construct