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High output v2 kit

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The High Output v2 kit is a laboratory equipment product offered by Illumina. It is designed to enable high-throughput DNA sequencing. The kit provides the necessary reagents and consumables required for the sequencing process. The core function of the kit is to facilitate the generation of high-quality sequencing data from DNA samples.

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Lab products found in correlation

Nextseq 500, by Illumina (29 mentions) Nebnext poly a mrna magnetic isolation module, by Illumina (8 mentions) Nextseq 500 platform, by Illumina (8 mentions) Nebnext ultra 2 directional rna library prep kit for, by Illumina (7 mentions) Qubit dsdna hs assay, by Thermo Fisher Scientific (5 mentions) Rneasy plus micro kit, by Qiagen (4 mentions) Standard sensitivity ngs fragment analysis kit, by Agilent Technologies (4 mentions) Nanodrop 1000 spectrophotometer, by Thermo Fisher Scientific (4 mentions) Basespace, by Illumina (3 mentions) Nebnext ultra directional rna library prep kit for, by Illumina (3 mentions) Truseq stranded mrna sample prep kit, by Illumina (3 mentions) High sensitivity rna analysis kit, by Agilent Technologies (3 mentions) Trio rna seq system, by Tecan (3 mentions) Quantseq 3 mrna seq library prep kit fwd for, by Illumina (3 mentions) Rneasy mini kit, by Qiagen (3 mentions) Qubit fluorometer, by Thermo Fisher Scientific (3 mentions) Nextseq 550, by Illumina (3 mentions) Truseq stranded mrna library prep kit, by Illumina (3 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (3 mentions) Rnaexpress app, by Illumina (2 mentions)

63 protocols using high output v2 kit

1

RNA-seq Protocol for Differential Gene Expression

Cited 1 time
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PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module, and bar-coded libraries were constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA). Libraries were pooled and single end sequenced (1 × 75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA). Raw data QC by FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and mapping to the mouse reference genome (mm10) by STAR57 (link) with default parameters were performed in Illumina BaseSpace (BaseSpace.illumina.com">https://BaseSpace.illumina.com). FeatureCounts58 (link) was used to count reads mapped to the annotated mouse genes. The EdgeR-based R pipeline in SARTools59 (link) was used to identify DEGs. DEGs with P < 0.01 and |log2Foldchange| > 2 are shown in the heatmap, and DEGs with P < 0.01 and |log2Foldchange| > 1 are included in IPA pathway analysis. Data obtained under this analysis was deposited in public dataset: GSE134412.
Scortegagna M., Hockemeyer K., Dolgalev I., Poźniak J., Rambow F., Li Y., Feng Y., Tinoco R., Otero D.C., Zhang T., Brown K., Bosenberg M., Bradley L.M., Marine J.C., Aifantis I, & Ronai Z.A. (2020). Siah2 control of T-regulatory cells limits anti-tumor immunity. Nature Communications, 11, 99.
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2

Capture Probe Sequencing on MiSeq and NextSeq

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Capture probe enriched sequencing libraries were sequenced on both the Illumina MiSeq and NextSeq 500. A MiSeq v3 Paired End 2 × 300 bp kit and a NextSeq500 2 × 150 bp High‐Output v2 kit (Illumina) were used, respectively, with a final library concentration of 10 and 1.6 pm, respectively, which included 5% PhiX control library.
All reads are available from NCBI sequencing read archive using project accession PRJNA349252.
Burridge A.J., Wilkinson P.A., Winfield M.O., Barker G.L., Allen A.M., Coghill J.A., Waterfall C, & Edwards K.J. (2017). Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum). Plant Biotechnology Journal, 16(4), 867-876.
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3

Quantitative Gene Expression Analysis

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After quantification using a Nanodrop 1000 spectrophotometer (Thermo Scientific), 1 μg of RNA was reverse- transcribed using random primers and MultiScribe Reverse Transcriptase (Applied Biosystems). Gene expression was analyzed by amplifying 50 ng of the complementary DNA using the CFX96 Real Time PCR Detection System with SYBR Green Master Mix (BioRad). The amplification parameters were set at 95 °C for 30 s, 58 °C for 30 s, and 72 °C for 30 s (40 cycles total). Gene expression values for each sample were normalized to the 18S RNA. RNASeq studies were performed in the Genomics Core at SBP Medical Discovery Institute. Briefly, total RNA was extracted from WPMY p62-KO (sgp62) and control (sgC) cells (n = 3, biological replicates) and from prostate tissue from 3 independent p62f/f and p62fspKO mice (n = 3 mice per genotype). PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA). Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA). Sequencing Fastq files were uploaded to BaseSpace and processed with RNAexpress App (Illumina) to obtain raw reads counts for each gene.
Linares J.F., Cordes T., Duran A., Reina-Campos M., Valencia T., Ahn C.S., Castilla E.A., Moscat J., Metallo C.M, & Diaz-Meco M.T. (2017). ATF4-induced metabolic reprograming is a synthetic vulnerability of the p62-deficient tumor stroma. Cell metabolism, 26(6), 817-829.e6.
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4

Genotyping-by-Sequencing Library Construction

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From the extracted DNA, genotyping-by-sequencing (GBS) libraries were built according to Poland et al. (2012) (link), containing 12 replicates for each parent. A total of 200 ng of genomic DNA per sample was digested with a combination of a rare-cutting enzyme (PstI) and a frequently cutting enzyme (MspI). DNA fragments were ligated to the common and barcode adapters, and the libraries were sequenced as 150-bp single-end reads using the High Output v2 Kit (Illumina, San Diego, CA, USA) for the NextSeq 500 platform (Illumina, San Diego, CA, USA).
Deo T.G., Ferreira R.C., Lara L.A., Moraes A.C., Alves-Pereira A., de Oliveira F.A., Garcia A.A., Santos M.F., Jank L, & de Souza A.P. (2020). High-Resolution Linkage Map With Allele Dosage Allows the Identification of Regions Governing Complex Traits and Apospory in Guinea Grass (Megathyrsus maximus). Frontiers in Plant Science, 11, 15.
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5

Genotyping-by-Sequencing of Forage Grasses

Cited 4 times
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Genotyping-by-sequencing (GBS) libraries of the U. decumbens and M. maximus progenies were built and sequenced as described by Ferreira et al. (2019 (link)) and Deo et al. (2020 (link)), respectively. For the progeny of U. humidicola, DNA was extracted following Vigna et al. (2016 (link)), and the GBS libraries were built according to Poland et al. (2012 (link)), containing five replicates for each parent and one for each hybrid. Genomic DNA (210 ng of DNA per individual) was digested using a combination of a rarely cutting enzyme (PstI) and a frequently cutting enzyme (MspI). Subsequently, the libraries were sequenced as 150-bp single-end reads using the High Output v2 Kit (Illumina, San Diego, CA, USA) in the NextSeq 500 platform (Illumina, San Diego, CA, USA). The quality of the resulting sequence data was evaluated using the FastQC toolkit (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Martins F.B., Moraes A.C., Aono A.H., Ferreira R.C., Chiari L., Simeão R.M., Barrios S.C., Santos M.F., Jank L., do Valle C.B., Vigna B.B, & de Souza A.P. (2021). A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses. Frontiers in Plant Science, 12, 737919.
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6

RNA-seq Transcriptome Analysis of Murine Samples

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PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illuminaâ (NEB, Ipswich MA). Libraries were pooled and single end sequenced (1×75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).
Read data was processed in BaseSpace (https://basespace.illumina.com). Reads were aligned to to Mus musculus genome (mm10) using STAR aligner (https://code.google.com/p/rna-star/) with default settings. Differential transcript expression was determined using the Cufflinks Cuffdiff package (Trapnell et al., 2010 (link)).
Differentially expressed genes were further analyzed using three different approaches: Ingenuity Pathway Analysis (IPA), Gene Set Enrichment Analysis (GSEA) (Subramanian et al., 2005 (link)), and Correlation Engine. Data were imported and analyzed in IPA using these parameter cut-offs: FPKM > 1; LogFoldChange > 2; p value < 0.01.
Sesillo F.B., Fox D, & Sacco A. (2019). Muscle Stem Cells Give Rise to Rhabdomyosarcomas in a Severe Mouse Model of Duchenne Muscular Dystrophy. Cell reports, 26(3), 689-701.e6.
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7

RNA-seq of BCR-ABL/NUP98-HOXA9 Leukemic Cells

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Lin− leukemic cells were sorted from mice transplanted with BCR-ABL/NUP98-HOXA9 transduced KLS cells. KLS cells were originally sorted from either WT or Sdc1−/− mice to generate WT or knockout leukemia, respectively. Total RNA was isolated using the RNeasy Micro Plus kit (QIAGEN). RNA libraries were generated from 150 ng of RNA using Illumina’s TruSeq Stranded mRNA Sample Prep Kit (Illumina). Libraries were pooled and single-end sequenced (1 × 75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina).
Spinler K., Bajaj J., Ito T., Zimdahl B., Hamilton M., Ahmadi A., Koechlein C.S., Lytle N., Kwon H.Y., Anower-E-Khuda F., Sun H., Blevins A., Weeks J., Kritzik M., Karlseder J., Ginsberg M.H., Park P.W., Esko J.D, & Reya T. (2020). A stem cell reporter based platform to identify and target drug resistant stem cells in myeloid leukemia. Nature Communications, 11, 5998.
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8

RNA-Seq Library Preparation and Sequencing

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RNA was extracted from pelleted cells using RNeasy Micro Kit (Cat. No. 74004, QIAGEN). RNA integrity (RIN ≥ 8.0) was confirmed using the High Sensitivity RNA Analysis Kit (DNF-472–0500, Agilent formerly AATI) on a 12-Capillary Fragment Analyzer. cDNA synthesis and Illumina sequencing libraries with 8-bp single indices were constructed from 10 ng total RNA using the Trio RNA-Seq System (0507–96, NuGEN). The resulting libraries were validated using the Standard Sensitivity NGS Fragment Analysis Kit (DNF-473–0500, Agilent formerly AATI) on a 12-Capillary Fragment Analyzer and quantified using Quant-it dsDNA assay kit (Cat. Q33120). Equal concentrations (2 nM) of libraries were pooled and subjected to paired-end (2×75) sequencing of approximately 40 million reads per sample using the High Output v2 kit (FC-404–2002, Illumina) on a NextSeq550 following the manufacturer’s instructions.
Huang A.Y., Woo J., Sardar D., Lozzi B., Huerta N.A., Lin C.C., Felice D., Jain A., Paulucci-Holthauzen A, & Deneen B. (2020). Region-specific transcriptional control of astrocyte function oversees local circuit activities. Neuron, 106(6), 992-1008.e9.
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9

Sex-Specific Transcriptional Profiling of Mouse Brain

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Total RNA sequencing was employed to study the expression profile of brain samples (right hemisphere) from male and female mice with respect to social rank-specific changes. The extracted RNA was sequenced at the Institute of Molecular Biology in Mainz, Germany. The Illumina TruSeq stranded total RNA Human/Mouse/Rat kit was used for library preparation containing RiboZero beads for rRNA depletion from total RNA. RNA integrity was measured prior to sequencing and all samples had RIN values above 8.2 (mean 8.78 ± 0.25). Sequencing was realized with the Illumina NextSeq 500 platform, and the High Output v2 kit with an average output of 32 million single-end (85 nt) reads per sample.
dos Santos Guilherme M., Tsoutsouli T., Todorov H., Teifel S., Nguyen V.T., Gerber S, & Endres K. (2021). N6 -Methyladenosine Modification in Chronic Stress Response Due to Social Hierarchy Positioning of Mice. Frontiers in Cell and Developmental Biology, 9, 705986.
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10

Organelle Fraction Isolation and NGS

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We extracted the organelle fraction with a reduced amount of nuclear DNA from leaves of 14-days-old sunflower seedlings as described by Makarenko et al. [29 (link)]. DNA isolation was performed with the PhytoSorb kit (Syntol, Russia), according to the manufacturer’s protocol. The NGS libraries were prepared with Nextera XT DNA Library Prep Kit (Illumina, USA), following the sample preparation protocol by Illumina. The concentration of the prepared library was measured with the Qubit fluorometer (Invitrogen, USA) and qPCR. Fragment length distribution was determined with Bioanalyzer 2100 (Agilent, USA). Libraries for NGS sequencing were diluted up to the concentration of 10 pM and sequenced on NextSeq 500 sequencer using High Output v2 kit (Illumina, USA). A total number of 10,174,497,150-bp paired reads were generated.
Makarenko M.S., Usatov A.V., Tatarinova T.V., Azarin K.V., Logacheva M.D., Gavrilova V.A, & Horn R. (2019). Characterization of the mitochondrial genome of the MAX1 type of cytoplasmic male-sterile sunflower. BMC Plant Biology, 19(Suppl 1), 51.
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