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Sureselectqxt target enrichment kit

Manufactured by Agilent Technologies
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The SureSelectQXT Target Enrichment kit is a laboratory tool used for the selective enrichment of specific DNA or RNA sequences from complex samples. It allows for the efficient capture and isolation of targeted genomic regions prior to sequencing analysis.

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Lab products found in correlation

Picogreen dsdna assay kit, by Thermo Fisher Scientific (2 mentions) Facsaria iib sorter, by BD (2 mentions) Genomeplex whole genome amplification kit, by Merck Group (2 mentions) Hiseq 2000 platform, by Illumina (2 mentions) Qiaamp dna micro kit, by Qiagen (2 mentions) Tapestation 4200, by Agilent Technologies (1 mentions) Qubit 4.0 fluorometer, by Illumina (1 mentions) Nextseq, by Illumina (1 mentions) Nexseq 500, by Illumina (1 mentions)

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SureSelectQXT

4 protocols using sureselectqxt target enrichment kit

1

Targeted Enrichment and Sequencing Protocol

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Genomic DNA from each sample was fragmented and used to prepare the NGS libraries for the Illumina platform using a hybridized capture-based target-enrichment approach (SureSelect) developed by Agilent Technologies. Regions of interest were enriched for each library using the SureSelectQXT Target Enrichment Kit following the manufacturer’s instructions (Agilent). Enriched DNA was precipitated with streptavidin-coated beads and washed, eluted, and amplified with index tags to identify each sample and pooled for sequencing. After quality control was measured by the 4200 TapeStation (Agilent) and quantified using Qubit® 4.0 Fluorometer, the libraries were sequenced on an Illumina NextSeq or MiSeq platform (Illumina Inc., San Diego, CA, USA). Paired-end sequencing (151-bp reads) was run. At the end of the process, this platform collects all the information in demultiplexed and paired FASTQ files for subsequent bioinformatic analysis.
Montaño A., Hernández-Sánchez J., Forero-Castro M., Matorra-Miguel M., Lumbreras E., Miguel C., Santos S., Ramírez-Maldonado V., Fuster J.L., de Las Heras N., García-de Coca A., Sierra M., Dávila J., de la Fuente I., Olivier C., Olazabal J., Martínez J., Vega-García N., González T., Hernández-Rivas J.M, & Benito R. (2020). Comprehensive Custom NGS Panel Validation for the Improvement of the Stratification of B-Acute Lymphoblastic Leukemia Patients. Journal of Personalized Medicine, 10(3), 137.
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2

Genomic profiling of myeloma cells

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BM myeloma PCs and CTCs were sorted from paired BM and PB from eight patients with symptomatic MM using a fluorescence-activated cell sorting FACSAria IIb sorter (BD Biosciences). Both tumor fractions were sorted according to the individual patient-specific aberrant phenotypes, and PB T lymphocytes were simultaneously collected for germline control. Genomic DNA was extracted using QIAamp DNA micro kit (QIAGEN) according to the manufacturer’s protocols, and double-stranded DNA concentration was quantified using PicoGreen dsDNA Assay kit (Life Technologies). The cell number of CTCs used and total amount of genomic DNA obtained are shown in Table S1.
For cases in which the total amount of DNA extracted from BM myeloma PCs (n = 1) and CTCs (n = 7) was limited, the genomic DNA was amplified using GenomePlex Whole Genome Amplification (WGA) Kits (Sigma-Aldrich) according to the manufacturer’s instructions. To capture the coding regions, we used the SureSelectQXT Target Enrichment kit (Agilent). All sequencing was performed on the Illumina HiSeq 2000 platform (Illumina) at the New York Genome Center or at the Broad Institute.
A detailed description of data processing is provided in the Supplemental Experimental Procedures.
Mishima Y., Paiva B., Shi J., Park J., Manier S., Takagi S., Massoud M., Perilla-Glen A., Aljawai Y., Huynh D., Roccaro A.M., Sacco A., Capelletti M., Detappe A., Alignani D., Anderson K.C., Munshi N.C., Prosper F., Lohr J.G., Ha G., Freeman S.S., Van Allen E.M., Adalsteinsson V.A., Michor F., San Miguel J.F, & Ghobrial I.M. (2017). The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma. Cell reports, 19(1), 218-224.
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3

Genomic profiling of myeloma cells

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BM myeloma PCs and CTCs were sorted from paired BM and PB from eight patients with symptomatic MM using a fluorescence-activated cell sorting FACSAria IIb sorter (BD Biosciences). Both tumor fractions were sorted according to the individual patient-specific aberrant phenotypes, and PB T lymphocytes were simultaneously collected for germline control. Genomic DNA was extracted using QIAamp DNA micro kit (QIAGEN) according to the manufacturer’s protocols, and double-stranded DNA concentration was quantified using PicoGreen dsDNA Assay kit (Life Technologies). The cell number of CTCs used and total amount of genomic DNA obtained are shown in Table S1.
For cases in which the total amount of DNA extracted from BM myeloma PCs (n = 1) and CTCs (n = 7) was limited, the genomic DNA was amplified using GenomePlex Whole Genome Amplification (WGA) Kits (Sigma-Aldrich) according to the manufacturer’s instructions. To capture the coding regions, we used the SureSelectQXT Target Enrichment kit (Agilent). All sequencing was performed on the Illumina HiSeq 2000 platform (Illumina) at the New York Genome Center or at the Broad Institute.
A detailed description of data processing is provided in the Supplemental Experimental Procedures.
Mishima Y., Paiva B., Shi J., Park J., Manier S., Takagi S., Massoud M., Perilla-Glen A., Aljawai Y., Huynh D., Roccaro A.M., Sacco A., Capelletti M., Detappe A., Alignani D., Anderson K.C., Munshi N.C., Prosper F., Lohr J.G., Ha G., Freeman S.S., Van Allen E.M., Adalsteinsson V.A., Michor F., San Miguel J.F, & Ghobrial I.M. (2017). The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma. Cell reports, 19(1), 218-224.
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4

EBV RNA Enrichment and Sequencing

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Sequencing libraries were constructed with SureSelect QXT Target Enrichment kit (Agilent Technologies, G9683B) and custom-designed EBV RNA bait probes (Agilent Technologies, 5190-4806), according to the manufacturer’s instructions. RNA bait probes were designed and kindly shared by Dr. Daniel P. Depledge [11 (link)]. EBV-enriched libraries were sequenced on a NexSeq500 Illumina device, with 300 cycle mid-output (2 × 150 bp) NextSeq Reagent kits v2 (Illumina Corporation, 20024905). FASTQ files of raw sequencing data were deposited in the NCBI database with the Sequence Read Archive (SRA) accession number PRJNA679281 (Supplemental Table S1).
Blazquez A.C., Berenstein A.J., Torres C., Izquierdo A., Lezama C., Moscatelli G., De Matteo E.N., Lorenzetti M.A, & Preciado M.V. (2021). Comprehensive Evolutionary Analysis of Complete Epstein–Barr Virus Genomes from Argentina and Other Geographies. Viruses, 13(6), 1172.
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