Nextseq 500 sequencing run

Manufactured by Illumina

The NextSeq 500 is a sequencing system designed for a wide range of sequencing applications. It utilizes sequencing-by-synthesis technology to generate high-quality sequencing data. The system is capable of producing up to 120 gigabases of data per run.

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Lab products found in correlation

Truseq stranded mrna sample preparation kit, by Illumina (1 mentions) High output v2 kit, by Illumina (1 mentions)

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NextSeq 500 (5724 citations) NextSeq (1155 citations) NextSeq sequencing (18 citations) NextSeq runs (6 citations)

3 protocols using nextseq 500 sequencing run

QuantSeq3′ mRNA-Seq Library Preparation

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All RNA samples were prepared with the QuantSeq3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH) following the standard supplier’s protocol for long fragments [20 (link)]. During the RNA removal step we also added globin blockers, so none of the abundant globin mRNA was copied to double stranded cDNA. The resulting cDNA libraries were equimolarly pooled, with up to 40 samples for one NextSeq 500 sequencing run (high output v2 kit, 150 cycli, single read, Illumina). This gave us an optimum of 10 million reads for each sample.

Bartholomeus E., De Neuter N., Lemay A., Pattyn L., Tuerlinckx D., Weynants D., Van Lede K., van Berlaer G., Bulckaert D., Boiy T., Vander Auwera A., Raes M., Van der Linden D., Verhelst H., Van Steijn S., Jonckheer T., Dehoorne J., Joos R., Jansens H., Suls A., Van Damme P., Laukens K., Mortier G., Meysman P, & Ogunjimi B. (2019). Diagnosing enterovirus meningitis via blood transcriptomics: an alternative for lumbar puncture?. Journal of Translational Medicine, 17, 282.

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Sex-Specific Osteocyte Gene Expression

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Differences in gene expression in the osteocyte cell population from male and female C57BL/6J mice were determined by RNASeq analysis (Marguerat and Bahler, 2010 (link); Wang et al., 2009 (link)). Osteocyte enriched preparations from male and female littermate mice were obtained and high quality nucleic acids were extracted. The Agilent Tape Station 2200 High Sensitivity RNA Assay was used to verify total RNA integrity (Agilent Technologies, Santa Clara, CA). RNA libraries were made using the Illumina TruSeq Stranded mRNA sample preparation kit following manufacturer protocol (Illumina, San Diego, CA) at the Center for Genome Innovation, Institute for Systems Genomics (University of Connecticut, Storrs, CT). Eight samples were individually barcoded, quantified using qPCR (KAPA Biosystems, Wilmington, MA), pooled in equimolar ratios and sequenced on High Output Illumina NextSeq 500 sequencing run (paired end 150bp reads; version 2 chemistry). The Computational Biology Core within the Institute for Systems Genomics at the University of Connecticut (Storrs, CT) performed quality control and data analyses on these samples.

Canalis E., Schilling L, & Zanotti S. (2016). Effects of Sex and Notch Signaling on the Osteocyte Cell Pool. Journal of cellular physiology, 232(2), 363-370.

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QuantSeq 3'mRNASeq Library Preparation

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The experimental set-up is similar to the workflow reported by Bartholomeus et al., 2018. (link) In brief, all RNA samples were prepared with the QuantSeq 3'mRNASeq Library Prep Kit FWD for Illumina (Lexogen GmbH) following the standard protocol for long fragments. The resulting cDNA libraries were equimolarly pooled, up to 40 samples for one NextSeq 500 sequencing run (high output v2 kit, 150 cycles, single read, Illumina).

Bartholomeus E., De Neuter N., Suls A., Elias G., van der Heijden S., Keersmaekers N., Jansens H., Van Tendeloo V., Beutels P., Laukens K., Ogunjimi B., Mortier G., Meysman P, & Van Damme P. (2020). Transcriptomic profiling of different responder types in adults after a Priorix® vaccination. Vaccine, 38(16).

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