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Nextseq device

Manufactured by Illumina
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The NextSeq device is a high-throughput sequencing system designed for a wide range of applications, including gene expression analysis, targeted resequencing, and epigenomics studies. The core function of the NextSeq device is to perform massively parallel DNA sequencing, enabling researchers to generate high-quality genomic data efficiently.

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Lab products found in correlation

Nextera dna sample prep kit, by Illumina (2 mentions) Umi second strand synthesis module for quantseq fwd, by Illumina (1 mentions) Tapestation, by Agilent Technologies (1 mentions)

Spelling variants of this product

NextSeq (1155 citations) NextSeq 500 device (41 citations) NextSeq 500 sequencing device (6 citations) NextSeq 2000 device (3 citations)

4 protocols using nextseq device

1

QuantSeq 3' mRNA-Seq Library Preparation

Cited 1 time
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The QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen Inc, Greenland, NH, USA) and the UMI Second Strand Synthesis Module for QuantSeq FWD (Illumina Inc, San Diego, CA, USA) were used to construct a sequencing library. The libraries were sequenced on a NextSeq device (Illumina Inc, San Diego, CA, USA) as a single-end 76. The unique molecular identifiers were removed from the raw reads with UMI-tools (v1.1.2). The quality and the length of the raw reads were inspected utilizing FastQC (v0.11.9) [19 ]. FastQ Screen (v0.15.0) [20 (link)] and a set of common lab organism genomes were used to check for putative contaminations. Up to 95% of the sequenced reads map on the bovine genome, whereas the non-bovine reads did not map to the tested lab organisms. The quality of the reads based on phred scores was good. Cutadapt (v3.7) [21 ] was used to trim the adaptors and filter reads containing ambiguities or reads that did not pass the phred score threshold of 20. Finally, the quality was checked with FastQc (v0.11.9) [19 ].
Vermeersch A.S., Ali M., Gansemans Y., Van Nieuwerburgh F., Geldhof P., Ducatelle R., Deforce D., Callens J, & Opsomer G. (2023). Severe udder cleft dermatitis lesion transcriptomics points to an impaired skin barrier, defective wound repair and a dysregulated inflammatory response as key elements in the pathogenesis. PLOS ONE, 18(7), e0288347.
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2

ATAC-seq Analysis of Pediatric MSCs

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ATAC-seq analysis on human pediatric MSCs was performed as recently described (Buenrostro et al., 2013 (link)). Briefly, 5×104 cells for each condition were first incubated in hypotonic buffer then resuspended in lysis buffer, centrifugated and resuspended in Transposase reaction mix for additional 30 min at 37°C, following manufacturer recommendations (Nextera DNA sample Prep Kit, Illumina). After DNA purification, adaptor sequences were added to the fragmented DNA by PCR. Purified PCR products were sequenced using the Illumina Nextseq device.
Boulay G., Sandoval G.J., Riggi N., Iyer S., Buisson R., Naigles B., Awad M.E., Rengarajan S., Volorio A., McBride M.J., Broye L.C., Zou L., Stamenkovic I., Kadoch C, & Rivera M.N. (2017). Cancer-Specific Retargeting of BAF Complexes by a Prion-like Domain. Cell, 171(1), 163-178.e19.
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3

ATAC-seq: Profiling Chromatin Accessibility

Cited 2 times
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ATAC-seq analysis was performed as recently described (56 (link)). Briefly, 5×104 cells for each condition were first incubated in hypotonic buffer then resuspended in lysis buffer, centrifugated and resuspended in Transposase reaction mix for additional 30 min at 37C, following manufacturer recommendations (Nextera DNA sample Prep Kit, Illumina). After DNA purification, adaptor sequences were added to the fragmented DNA by PCR. Purified PCR products were sequenced using the Illumina Nextseq device. Paired end reads were aligned to hg19 using BWA (48 (link)). Read start sites were adjusted to represent the center of the transposon binding event (+4 bp in the plus strand and −5 bp in the minus strand). Signal densities were calculated over a sliding 150 bp window at 20 bp steps and normalized to 10M reads in each experiment.
Boulay G., Awad M.E., Riggi N., Archer T.C., Iyer S., Boonseng W.E., Rossetti N.E., Naigles B., Rengarajan S., Volorio A., Kim J.C., Mesirov J.P., Tamayo P., Pomeroy S.L., Aryee M.J, & Rivera M.N. (2017). OTX2 activity at distal regulatory elements shapes the chromatin landscape of Group 3 medulloblastoma. Cancer discovery, 7(3), 288-301.
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4

CAGE Library Generation from Total RNA

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Total and nascent RNAs were harvested from TBX-4B cells as previously described [31 (link)]. CAGE libraries were generated using CAGE library preparation kit (KK DNAFORM) following the manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 5 μg of total RNA using random primers. The cap at the 5′end of the RNAs was biotinylated to facilitate the subsequent cap-trapping step. Remaining RNA fragments were digested with RNaseONE enzyme. Approximately 10 ng of each cDNA was used for linker ligation and library preparation. CAGE libraries were quantified by qPCR and size distribution was evaluated by TapeStation (Agilent Technologies) before sequencing in a NextSeq device (Illumina) as described previously [52 (link)]. NET-CAGE was performed as described previously [31 (link)]. We added the step to separate nuclear RNA and cytoplasmic RNA before we performed CAGE protocol.
Miyazato P., Matsuo M., Tan B.J., Tokunaga M., Katsuya H., Islam S., Ito J., Murakawa Y, & Satou Y. (2019). HTLV-1 contains a high CG dinucleotide content and is susceptible to the host antiviral protein ZAP. Retrovirology, 16, 38.
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