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Hiseq x pe150

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The HiSeq X PE150 is a high-throughput sequencing system designed for whole-genome sequencing. It can generate up to 1.8 terabases of data per run, with read lengths of up to 150 base pairs paired-end.

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Lab products found in correlation

Truseq stranded mrna library prep kit, by Illumina (1 mentions) Rnase a treatment, by Thermo Fisher Scientific (1 mentions) Deep well reaction module, by Bio-Rad (1 mentions) C1000 touch thermal cycler, by Bio-Rad (1 mentions) Qubit dsdna br assay kit, by Thermo Fisher Scientific (1 mentions) Truseq nano dna library prep, by Illumina (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions) Qiaamp blood mini kit, by Qiagen (1 mentions) 3730 dna analyzer, by Thermo Fisher Scientific (1 mentions) Hiseq 2000, by Illumina (1 mentions)

Close spelling variants of this product

HiSeq X 10-PE150 platform HiSeq X-ten PE150 sequencing Illumina Hiseq X ten sequencer (PE150 mode) HiSeq X Ten PE150 platform HiSeq X Ten PE150 HiSeq PE150 HiSeq X PE150

5 protocols using hiseq x pe150

1

Illumina-Based RNA-Seq Library Preparation and Analysis

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Illumina's TruSeq Stranded mRNA Library Prep Kit was used to prepare the six independent libraries (three for galls and three for uninfected controls). Samples were dual‐indexed for post‐sequencing demultiplexing, pooled in equimolar amounts and sequenced in a fraction of an Illumina® HiSeq X PE150 by AllGenetics & Biology SL, A Coruña, Spain. A description of the DEGs acquired in TAIR10 and additional details are provided in Table S3.
RNA‐sequencing raw data and detailed data processing are available via GEO accession number GSE155171 and in Methods S1. Differential expression analysis was performed with deseq2 (v.1.20.0; Love et al., 2014 (link)) using R (v.3.5.2; R Core Team, 2018 ) and Rstudio (v.1.1.463; RStudio Team, 2018 ). Genes with a ¦log2‐fold change¦ > 0.5 and an adjusted P‐value < 0.01 were considered differentially expressed (DEGs).
The 3 dpi sRNA libraries (GEO accession number GSE71563) were generated as described by Cabrera et al. (2016 (link)) (Table S4; Methods S1).
Silva A.C., Ruiz‐Ferrer V., Müller S.Y., Pellegrin C., Abril‐Urías P., Martínez‐Gómez Á., Gómez‐Rojas A., Berenguer E., Testillano P.S., Andrés M.F., Fenoll C., Eves‐van den Akker S, & Escobar C. (2022). The DNA methylation landscape of the root‐knot nematode‐induced pseudo‐organ, the gall, in Arabidopsis, is dynamic, contrasting over time, and critically important for successful parasitism. The New Phytologist, 236(5), 1888-1907.
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2

Whole Genome Sequencing of Arabidopsis

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Total DNA was isolated from ~400 mg pools of leaves from 14-d-old plants grown on soil using the CTAB DNA extraction protocol [40 ] plus RNAse A treatment (Fermentas). Libraries were prepared from the DNA samples using the NxSeq AmpFREE Low DNA Library kit (LuciGen, Cat. #14000–2) as per the manufacturer’s protocol. This includes SPRI bead cleanup and size selection steps for a final median insert size of ~320 bp. Sequencing was performed on the Illumina HiSeq X PE150 (paired-end, 150bp). Library preparation and sequencing were done at Génome Québec (McGill University, Montréal, Qc, Canada). All datasets were made available on NCBI SRA (Project number: PRJNA482863).
Pérez Di Giorgio J.A., Lepage É., Tremblay-Belzile S., Truche S., Loubert-Hudon A, & Brisson N. (2019). Transcription is a major driving force for plastid genome instability in Arabidopsis. PLoS ONE, 14(4), e0214552.
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3

Single-Cell RNA Sequencing Using 10X Genomics

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The scRNA-Seq libraries were prepared from individual cells using the 10X Genomics platform. The Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237), Chromium Single Cell 3’ Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturer’s instructions. Briefly, for each sample, approximately 9000 cells were loaded onto the 10X Genomics Chromium Controller machine for Gel Beads-in-Emulsion (GEM) generation. Reverse transcription was performed using a C1000 Touch Thermal Cycler with a Deep Well Reaction Module (Bio-Rad) using the following program: 55 °C for 2 h; 85 °C for 5 min; hold 4 °C. cDNA was recovered, purified, and amplified to generate sufficient quantities for library preparation. All single-cell libraries were sequenced on the Illumina Hiseq X (PE150).
Dinh H.Q., Pan F., Wang G., Huang Q.F., Olingy C.E., Wu Z.Y., Wang S.H., Xu X., Xu X.E., He J.Z., Yang Q., Orsulic S., Haro M., Li L.Y., Huang G.W., Breunig J.J., Koeffler H.P., Hedrick C.C., Xu L.Y., Lin D.C, & Li E.M. (2021). Integrated single-cell transcriptome analysis reveals heterogeneity of esophageal squamous cell carcinoma microenvironment. Nature Communications, 12, 7335.
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4

Comprehensive Genomic Profiling of FFPE and Blood

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The genomic DNA (gDNA) was extracted from the FFPE tissue using the proprietary method of Wuxi (NextCODE SeqPlus extraction protocol) and from the FF tissue with QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s instructions. gDNA was extracted from a 200 μL EDTA-whole blood sample using the QIAamp® Blood Mini Kit (Qiagen) with QIAcube according to the manufacturer’s instructions. The DNA samples were quantified with a Qubit 3.0 fluorescence spectrometer (Life Technologies, Waltham, MA USA) using a Qubit dsDNA BR assay kit. Covaris has been used for DNA shearing. TruSeq® Nano DNA Library Prep (Illumina) has been used for library construction. The Illumina sequencing platform HiSeqX PE150 has been used for WGS. The mean coverage was of 30X for the blood sample and 100X for the tumor samples.
de Schaetzen van Brienen L., Larmuseau M., Van der Eecken K., De Ryck F., Robbe P., Schuh A., Fostier J., Ost P, & Marchal K. (2020). Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples. BMC Medical Genomics, 13, 94.
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5

Whole Genome Sequencing of Listeria monocytogenes Strain

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The whole genome of L. monocytogenes strain ICDC-LM188 was determined by using the Illumina HiSeq 2000 platform. The reads were assembled de novo into a high-quality draft genome using Velvet (version 1.2.10) with default parameters and with an average 85-fold sequencing coverage. All of the gaps were closed by primer walking and sequencing of PCR products using Applied Biosystems 3730 DNA Analyzer. Genome annotation was performed using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP). Whole-genome shotgun sequencing of the other 70 ST87 L. monocytogenes strains was performed on the Illumina HiSeq X PE150 platform. The read quality was assessed with FastQC, and the reads were filtered to remove low-quality sequences (quality score ≤ 38), ambiguous reads (reads with 10 or more unknown base N) and adapter sequences. High-quality paired-end reads were assembled into scaffolds using SOAPdenovo v1.05. The coding genes were retrieved using the GeneMarkS (version 4.17, http://topaz.gatech.edu/)program [43 (link)] or Rapid Annotations based on Subsystem Technology (RAST) server (version 2, http://rast.nmpdr.org/rast.cgi) [44 (link)]. The database of Clusters of Orthologous Groups of proteins (COGs) was used to predict gene functions and the parameters for BLASTP searches were E-value of less than 10− 5 and larger than 40% of the query coverage.
Wang Y., Luo L., Li Q., Wang H., Wang Y., Sun H., Xu J., Lan R, & Ye C. (2019). Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China. BMC Genomics, 20, 1014.
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