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Hiseqxten pe150

Manufactured by Novogene
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The HiseqXten-PE150 is a high-throughput sequencing platform capable of generating paired-end reads of up to 150 base pairs in length. It utilizes Illumina's sequencing-by-synthesis technology to provide accurate and reliable DNA sequencing data.

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Lab products found in correlation

Nebnext poly a mrna magnetic isolation module kit, by New England Biolabs (1 mentions) Monarch total rna miniprep kit, by New England Biolabs (1 mentions) Nebnext ultra rna library prep kit for, by Illumina (1 mentions) Qiaamp dna blood mini kit, by Qiagen (1 mentions) Trueprep dna library prep kit v2, by Illumina (1 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (1 mentions) Vahtstm dna clean beads, by Vazyme (1 mentions)

7 protocols using hiseqxten pe150

1

Whole-Genome Sequencing of Tomato Mutants

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Individuals (>30) exhibiting the su mutant-like phenotype and individuals (>30) exhibiting the WT phenotype were collected from the F2 population generated by crossing the su mutant and LA1589. Their genomic DNA was extracted by CTAB. Two micrograms of DNA was mixed to construct two samples (mutant-like and WT samples). Genome sequencing of the two samples was performed by HiSeqXten-PE150 (Novogene, Beijing) with a depth of 30× coverage of the tomato genome. The candidate region was analyzed according to the method in ref. 49 (link).
Chang J., Zhang F., Qin H., Liu P., Wang J, & Wu S. (2021). Mutation of SlARC6 leads to tissue-specific defects in chloroplast development in tomato. Horticulture Research, 8, 127.
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2

Bulk Segregant Analysis for Mutant Identification

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Genomic DNA of 30 individuals clearly exhibiting mutant-like phenotypes from F2 population and 30 WT individuals was extracted by CTAB. All DNA quality and concentration were checked and then mixed to construct two bulks (mutant-like bulk; WT bulk). Each bulk was sequenced to a depth of 30× coverage of the tomato genome by HiseqXten-PE150 (Novogene). Trimmed sequences are mapped onto the tomato reference genome (Heinz 1706 cultivar) and EMS mutation variants are filtered. Analysis of the allelic variant frequencies in the pools leads to the identification of the causal mutation with very high frequency in the mutant-like bulk (ideally 100% having the variant allele). The genes with the expected allelic frequency tend to be 1 for the mutant-like bulk was performed mutation identification and transgenic verification [47 (link)]. Then, the candidate genes were cloned and sequenced to verify the mutant site. The primers were listed in the S3 Table.
Chang J., Xu Z., Li M., Yang M., Qin H., Yang J, & Wu S. (2019). Spatiotemporal cytoskeleton organizations determine morphogenesis of multicellular trichomes in tomato. PLoS Genetics, 15(10), e1008438.
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3

RNA-seq of T cell transcriptome

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RNA of T cells (0.2 million cells per sample) was extracted using the Monarch Total RNA Miniprep Kit (NEB, T2010S). After quality analysis, mRNA enrichment was carried out with NEBNext Poly(A) mRNA Magnetic Isolation Module kit (NEB, E7490L) and bulk RNA-seq libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L). All experimental procedures followed the manufacturer’s specification. All libraries were sequenced on an Illumina Hiseq Xten-PE150 (Novogene) according to the manufacturer’s instruction.
Lu J., Wang X., Sun K, & Lan X. (2021). Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data. Briefings in Bioinformatics, 22(6), bbab181.
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4

Whole Exome Sequencing of Patient Blood

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Total genomic DNA was extracted from the 200 μL whole blood of the patient and his parents using the QIAamp DNA blood mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. About 5 µg of purified DNA was diluted in 200 µL of buffer AE. Whole-exome sequencing was performed on a HiSeq X ten PE150 by Novogene Co., Ltd. (Shanghai, China). The resulting data were analyzed and annotated using the DNAnexus (https://www.dnanexus.com/ 20 March 2020) data storage and analysis facility.
Man Y., Shang X., Liu C., Zhang W., Huang Q., Ma S., Shiang R., Zhang F., Zhang L, & Zhang Z. (2022). Whole-Exome Sequencing Identifies the VHL Mutation (c.262T > C, p.Try88Arg) in Non-Obstructive Azoospermia-Associated Cystic Renal Cell Carcinoma. Current Oncology, 29(4), 2376-2384.
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5

ATAC-seq Protocol for Mouse Oligodendrocyte Precursor Cells

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In brief, 50,000 mouse OPCs were washed once with cold PBS and resuspended in 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630) to isolate nuclei. The suspension of nuclei was then centrifuged for 10 min at 500 g at 4°C, followed by the addition of 50 μL transposition reaction mix (10 μL 5 × TTBL, 5 μL TTE Mix V50 and 35 μL nuclease-free H2O) of TruePrep™ DNA Library Prep Kit V2 for Illumina’s instructions (TD501, Vazyme). Samples were then PCR amplified and incubated at 37°C for 30 min. DNA was isolated using VAHTSTM DNA Clean Beads (Vazyme #N411). ATAC-seq libraries were first subjected to 15 cycles of pre-amplification. Libraries were purified with a VAHTSTM DNA Clean Beads. Library concentration was measured using a Qubit™ dsDNA HS Assay Kit (Invitrogen, Q32854) according to the manufacturer’s instructions. Finally, the ATAC library was sequenced on an illumina Hiseq-Xten PE150 by Novogene to generate 2× 150-bp paired-end reads.
Liu Z., Yan M., Liang Y., Liu M., Zhang K., Shao D., Jiang R., Li L., Wang C., Nussenzveig D.R., Zhang K., Chen S., Zhong C., Mo W., Fontoura B.M, & Zhang L. (2019). Nucleoporin Seh1 Interacts with Olig2/Brd7 to Promote Oligodendrocyte Differentiation and Myelination. Neuron, 102(3), 587-601.e7.
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6

Bulked Segregant Analysis for Trait Mapping

Cited 1 time
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Bulked segregant analysis was performed according to Chang et al. [50 (link)]. The slf homozygous plants were used as female parent and crossed to the WT. The F1 plants were then selfed to generate F2 mapping population. For BSA-seq, we extracted genomic DNA from 28 slf mutant individuals and 30 WT individuals in the F2 mapping population using CTAB method [51 (link)]. All DNA quality and concentration were checked before being mixed to construct two bulks (slf bulk and WT bulk). The slf bulk and WT bulk were sequenced to a depth of 28× and 30× coverage of the tomato genome by HiseqXten-PE150 (Novogene). Trimmed sequences are mapped onto the tomato reference genome (Heinz 1706 cultivar) and mutation variants are filtered. Analysis of the allelic variant frequencies in the pools led to the identification of the causal mutation with 100% frequency in the slf bulk. The genes with the expected allelic frequency of 1 were further examined and we conducted transgenic verification for the identified candidate gene. The candidate genes were cloned and sequenced to verify the mutations. The primers were listed in the S1 Table.
Yang L., Qi S., Touqeer A., Li H., Zhang X., Liu X, & Wu S. (2020). SlGT11 controls floral organ patterning and floral determinacy in tomato. BMC Plant Biology, 20, 562.
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7

Mapping Mutant Hair Phenotype in Tomato

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Mapping populations were constructed by crossing the short hair mutant and WT. The F2 plants (>200) were used for the phenotype segregation analysis. The genomic DNA of individuals exhibiting mutant‐like phenotypes (>30) and individuals with WT‐like phenotypes (>30) were extracted by CTAB. 2 μg DNA of individuals was mixed to construct two bulks (mutant‐like bulk and WT‐like bulk). Two bulks were sequenced (>30× coverage of the tomato genome) by HiseqXten‐PE150 (Novogene). Trimmed sequences were mapped onto the tomato reference genome. The allelic variant frequencies were analysed and the SNPs with high frequency were identified based on the previous reports (Chang et al., 2019; Garcia et al., 2016).
Hua B., Chang J., Wu M., Xu Z., Zhang F., Yang M., Xu H., Wang L., Chen X, & Wu S. (2020). Mediation of JA signalling in glandular trichomes by the woolly/SlMYC1 regulatory module improves pest resistance in tomato. Plant Biotechnology Journal, 19(2), 375-393.
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