Nebnext kits

Manufactured by New England Biolabs

Sourced in United States

NEBNext kits are a collection of reagents and protocols designed for various genomic applications, including library preparation, DNA and RNA sequencing, and target enrichment. The kits provide a streamlined workflow and consistent performance to enable efficient and reliable sample processing.

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Lab products found in correlation

Hiseq 2500, by New England Biolabs (1 mentions) Maxwell tissue dna purification kit, by Promega (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Hiseq 2000, by Illumina (1 mentions) Picogreen fluorescence assay, by Thermo Fisher Scientific (1 mentions) Ampure xp bead, by Beckman Coulter (1 mentions)

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3 protocols using nebnext kits

FoundationOne®HEME Sequencing Assay

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Next-generation sequencing: The FoundationOne^®HEME assay, a hybrid capture methodology detecting base substitutions, insertions, deletions, and copy number (CN) alterations in up to 406 genes and gene rearrangements in up to 265 genes, tumor mutation burden and microsatellite instability was used as in previously described methods [14 (link)]. DNA and RNA were extracted using the Maxwell^® Tissue DNA Purification Kit (Promega AS1030). Library construction was done using NEBNext kits (NEB E6040S) and the sequencing was performed on a HiSeq2500 according to clinical laboratory standards with 150-base pair paired-end reads (Department of Pathology and Molecular Pathology, University Hospital Zurich, Switzerland).

Harnisch K., Steiner S., Pliego-Mendieta A., Chen Y., Planas-Paz L, & Pauli C. (2023). Establishment and functional testing of a novel ex vivo extraskeletal osteosarcoma cell model (USZ20-ESOS1). Human Cell, 37(1), 356-363.

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RNA-seq Analysis of PBMCs and iPSC-Derived Macrophages

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Total RNA was isolated from sorted cells using Qiazol lysis reagent and RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA degradation was analyzed on RNA Pico chips using Agilent Bioanalyzer 2100 (Agilent) and RNA integrity number (RIN) was calculated (18 (link)). For primary PBMCs, Illumina RNA-Seq and data analysis was done as previously described (54 (link)). For iPSC-derived macrophages, poly-A tailed mRNA isolation, library preparation and quantification were performed with NEBNext kits (New England Biolabs, Ipswich, USA) following manufacturer’s instructions. Libraries were sequenced on a Lumin (Illumina, San Diego, USA) and transcriptome analysis was performed as previously described (55 (link)). Differentially expressed genes were assessed by edgeR and pathway analysis was performed by gene set enrichment analysis (GSEA) as previously described (56 (link), 57 (link)).

Magg T., Okano T., Koenig L.M., Boehmer D.F., Schwartz S.L., Inoue K., Heimall J., Licciardi F., Ley-Zaporozhan J., Ferdman R.M., Caballero-Oteyza A., Park E.N., Calderon B.M., Dey D., Kanegane H., Cho K., Montin D., Reiter K., Griese M., Albert M.H., Rohlfs M., Gray P., Walz C., Conn G.L., Sullivan K.E., Klein C., Morio T, & Hauck F. (2021). Heterozygous OAS1 Gain-of-Function Variants Cause an Autoinflammatory Immunodeficiency. Science immunology, 6(60), eabf9564.

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Targeted Cancer Gene Sequencing

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Next-generation sequencing assays were conducted as described previously [19 (link)]. In brief, DNA was extracted from FFPE sections and quantified by a PicoGreen fluorescence assay (Invitrogen). DNA fragmentation was performed by sonication, followed by purification using the AMPure XP Beads (Agencourt). Sequencing libraries were constructed with the NEBNext kits (NEB), amplified with HiFi (Kapa), quantified by qPCR (Kapa SYBR Fast), and sized on a LabChip GX (Caliper). Hybridization was done using a pool of 23,685 individually synthesized oligonucleotides (Integrated DNA Technology), which targeted exons of 287 cancer genes and introns of 19 fusion genes. The captured library was amplified, purified, quantified by qPCR (Kapa), and sized on a LabChip GX (Caliper). Normalized libraries were pooled and sequenced on the Illumina HiSeq 2000 instrument.

Xu X., Li J., Gao Y., Lv W., Wei Q., Tang X., Hu J., Yuan X., Wu W., Zhang L., Luo C., Chen L., Ying J., Zhu X, & Xu Q. (2022). Associations of Clinical and Molecular Characteristics with the Response to Immune Checkpoint Blockade in Advanced Gastric Cancers. Journal of Oncology, 2022, 2162229.

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