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Agilent technologies sureselect xt reagent kit
Sureselect Xt Reagent Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 95/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 95 stars, based on 12 article reviews
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sureselect xt reagent kit - by Bioz Stars, 2020-02
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Amplification:

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols. .. For scRNA-seq, CD138-enriched cells were subjected to single cell capture and cDNA amplification using the C1 single-cell auto prep system (Fluidigm) with the SMARTer kit (Clontech).

Article Title: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: Genomic DNA from 12 nodules and their corresponding cirrhotic tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of a library using SureSelect XT Human All Exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol. .. Briefly, a paired-end DNA sequencing library was prepared by genomic DNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

Article Title: PI3K as a potential therapeutic target in thymic epithelial tumors
Article Snippet: MP57 samples and IU-TAB1 sheared DNA samples were constructed into individual libraries using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA) or the Personal Genome Diagnostics (PGDx) custom library kit (PGDx, Baltimore, MD), according to the manufacturers’ protocols. .. A unique index tag was added to each library sample by a 12-cycle PCR amplification.

Article Title: Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers
Article Snippet: Genomic DNA was sheared using the Covaris S220 (Covaris, Woburn, MA) to construct a sequencing library using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) on target genes. .. A paired-end sequencing library was purified and amplified with a barcode tag, and the library quality and quantity were determined.

Article Title: Circulating tumor DNA shows variable clonal response of breast cancer during neoadjuvant chemotherapy
Article Snippet: The sequencing libraries for primary tumor tissue samples were created by using SureSelect XT reagent kit, HSQ (Agilent Technologies) following the manufacturer’s recommended protocols. .. DNA fragments were ligated with pre-indexed PentAdapter™ (PentaBase ApS, Denmark) at 4°C overnight, purified using AMPure XP beads (Beckman Coulter, Indianapolis, IN, USA), amplified with P5 and P7 oligonucleotides, and subjected to hybrid selection for target enrichment.

Synthesized:

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: .. A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using a SureSelect XT Reagent kit (Agilent Technologies, Santa Clara, CA), Each library was synthesized with sample-specific barcodes of 6 bp, quantified using PicoGreen, and four libraries were pooled to a total of 600 ng for hybrid capture using an Agilent SureSelectXT custom kit (OPv2 RNA bait, 2.9 Mb; Agilent Technologies). .. The concentration of the enriched target was measured by quantitative polymerase chain reaction (PCR) (Kapa Biosystems, Woburn, MA), and loaded on the MiSeq platform (Illumina Inc., San Diego, CA) for paired end sequencing.

Construct:

Article Title: Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application
Article Snippet: A DNA library was prepared as described in our previous report using the S1 method ; briefly, gDNA shearing with S1 enzyme, end repair, A-tailing, and ligation with the TruSeq adaptor using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA, USA). .. Each library was constructed with sample-specific barcodes 6 bp in size and quantified using the Qubit kit.

Article Title: Clinical Relevance of Genomic Changes in Recurrent Pediatric Solid Tumors
Article Snippet: .. Genomic DNA (250 ng) from each tissue was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn, MA) and used to construct a library using CancerSCAN , probes and a SureSelect XT reagent kit (HSQ; Agilent Technologies) according to the manufacturer's protocol. ..

Article Title: PI3K as a potential therapeutic target in thymic epithelial tumors
Article Snippet: .. MP57 samples and IU-TAB1 sheared DNA samples were constructed into individual libraries using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA) or the Personal Genome Diagnostics (PGDx) custom library kit (PGDx, Baltimore, MD), according to the manufacturers’ protocols. .. Each library was hybridized to RNA baits from the SureSelect Human Kinome v1 panel (Agilent Technologies, Santa Clara, CA, USA) or our PGDx custom gene panel (PGDx, Balitmore, MD) for 24 hours and captured using streptavidin-coated beads.

Article Title: Clinical Relevance of Genomic Changes in Recurrent Pediatric Solid Tumors
Article Snippet: .. Sequencing Using a Cancer Panel (CancerSCAN) Genomic DNA (250 ng) from each tissue was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn, MA) and used to construct a library using CancerSCAN , probes and a SureSelect XT reagent kit (HSQ; Agilent Technologies) according to the manufacturer's protocol. ..

Article Title: Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers
Article Snippet: .. Genomic DNA was sheared using the Covaris S220 (Covaris, Woburn, MA) to construct a sequencing library using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) on target genes. .. A paired-end sequencing library was purified and amplified with a barcode tag, and the library quality and quantity were determined.

Article Title: Circulating tumor DNA shows variable clonal response of breast cancer during neoadjuvant chemotherapy
Article Snippet: The sequencing libraries for primary tumor tissue samples were created by using SureSelect XT reagent kit, HSQ (Agilent Technologies) following the manufacturer’s recommended protocols. .. Sequencing libraries for PBL and plasma DNAs were constructed with KAPA Hyper Prep kits (Kapa Biosystems, Woburn, MA, USA) [ ].

Real-time Polymerase Chain Reaction:

Article Title: Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application
Article Snippet: A DNA library was prepared as described in our previous report using the S1 method ; briefly, gDNA shearing with S1 enzyme, end repair, A-tailing, and ligation with the TruSeq adaptor using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA, USA). .. The concentration of the enriched target was measured using quantitative polymerase chain reaction (qPCR; Kapa Biosystems, Inc., Woburn, MA, USA).

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using a SureSelect XT Reagent kit (Agilent Technologies, Santa Clara, CA), Each library was synthesized with sample-specific barcodes of 6 bp, quantified using PicoGreen, and four libraries were pooled to a total of 600 ng for hybrid capture using an Agilent SureSelectXT custom kit (OPv2 RNA bait, 2.9 Mb; Agilent Technologies). .. The concentration of the enriched target was measured by quantitative polymerase chain reaction (PCR) (Kapa Biosystems, Woburn, MA), and loaded on the MiSeq platform (Illumina Inc., San Diego, CA) for paired end sequencing.

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA, USA). .. The concentration of the enriched target was measured by quantitative PCR (Kapa Biosystems, Inc., Woburn, MA, USA), and samples were loaded onto the MiSeq platform for paired-end sequencing.

Formalin-fixed Paraffin-Embedded:

Article Title: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: Paragraph title: Genomic DNA preparation from FFPE tissues for WES ... Genomic DNA from 12 nodules and their corresponding cirrhotic tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of a library using SureSelect XT Human All Exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol.

Article Title: Four distinct immune microenvironment subtypes in gastric adenocarcinoma with special reference to microsatellite instability
Article Snippet: .. Deep targeted sequencing of DNA Genomic DNA (250 ng) from FFPE tissue was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn, Massachusetts, USA) and used for library construction with SureSelect XT reagent kit, HSQ (Agilent Technologies, Santa Clara, California, USA) based on the manufacturer’s protocol. ..

Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
Article Snippet: This was chosen due to the difficulty in biopsying AVMs due to risk of bleeding and because this panel is optimized for FFPE tissue. .. DNA library preparation was performed for each sample using the Agilent SureSelect XT Reagent Kit per the manufacturer’s protocol ( http://www.ogt.co.uk/assets/0000/4457/990162_HB_SureSeqSolidTumour_110215.pdf ).

Ligation:

Article Title: Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application
Article Snippet: .. A DNA library was prepared as described in our previous report using the S1 method ; briefly, gDNA shearing with S1 enzyme, end repair, A-tailing, and ligation with the TruSeq adaptor using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA, USA). .. Each library was constructed with sample-specific barcodes 6 bp in size and quantified using the Qubit kit.

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: .. A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using a SureSelect XT Reagent kit (Agilent Technologies, Santa Clara, CA), Each library was synthesized with sample-specific barcodes of 6 bp, quantified using PicoGreen, and four libraries were pooled to a total of 600 ng for hybrid capture using an Agilent SureSelectXT custom kit (OPv2 RNA bait, 2.9 Mb; Agilent Technologies). .. The concentration of the enriched target was measured by quantitative polymerase chain reaction (PCR) (Kapa Biosystems, Woburn, MA), and loaded on the MiSeq platform (Illumina Inc., San Diego, CA) for paired end sequencing.

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: .. A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA, USA). ..

Article Title: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: Genomic DNA from 12 nodules and their corresponding cirrhotic tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of a library using SureSelect XT Human All Exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol. .. Briefly, a paired-end DNA sequencing library was prepared by genomic DNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

Generated:

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols. .. Sequencing libraries were generated and multiplexed using Nextera XT DNA sample prep kit (Illumina) and sequenced on the HiSeq 2500 in the 100-bp paired-end mode of the TruSeq rapid PE cluster kit and TruSeq rapid SBS kit following the Smart-seq2 protocol ( ).

DNA Sequencing:

Article Title: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: Genomic DNA from 12 nodules and their corresponding cirrhotic tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of a library using SureSelect XT Human All Exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol. .. Briefly, a paired-end DNA sequencing library was prepared by genomic DNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

Polymerase Chain Reaction:

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using a SureSelect XT Reagent kit (Agilent Technologies, Santa Clara, CA), Each library was synthesized with sample-specific barcodes of 6 bp, quantified using PicoGreen, and four libraries were pooled to a total of 600 ng for hybrid capture using an Agilent SureSelectXT custom kit (OPv2 RNA bait, 2.9 Mb; Agilent Technologies). .. The concentration of the enriched target was measured by quantitative polymerase chain reaction (PCR) (Kapa Biosystems, Woburn, MA), and loaded on the MiSeq platform (Illumina Inc., San Diego, CA) for paired end sequencing.

Article Title: Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker
Article Snippet: Whole exome sequencing and data analysis Genomic DNA (1 μg) from the bone marrow and matching blood samples was sheared by Covaris S220 (Covaris, MA, USA) and used for library construction with SureSelect XT Human All Exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer's protocols. .. PCR duplications are marked by Picard-tools-1.8 ( http://picard.sourceforge.net/ ), data cleanup was followed by GATK, and variants were identified with GATK-2.2.9 ( https://www.broadinstitute.org/gatk/ ).

Article Title: PI3K as a potential therapeutic target in thymic epithelial tumors
Article Snippet: MP57 samples and IU-TAB1 sheared DNA samples were constructed into individual libraries using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA) or the Personal Genome Diagnostics (PGDx) custom library kit (PGDx, Baltimore, MD), according to the manufacturers’ protocols. .. A unique index tag was added to each library sample by a 12-cycle PCR amplification.

Sonication:

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: Targeted Next Generation Sequencing Targeted NGS was performed using the MiSeq platform (Illumina, San Diego, CA, USA) with OncoPanel version 2 (OPv2) for capturing exons of 505 cancer-related genes plus partial introns from 15 genes often rearranged in cancer . gDNA 200 ng was fragmented by sonication (Covaris Inc., Woburn, MA) to an average of 250 bp, followed by size selection using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, UK). .. A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using a SureSelect XT Reagent kit (Agilent Technologies, Santa Clara, CA), Each library was synthesized with sample-specific barcodes of 6 bp, quantified using PicoGreen, and four libraries were pooled to a total of 600 ng for hybrid capture using an Agilent SureSelectXT custom kit (OPv2 RNA bait, 2.9 Mb; Agilent Technologies).

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: Genomic DNA (200 ng) from normal small intestine mucosa was fragmented to 250 bp by sonication (Covaris Inc., Woburn, MA, USA), followed by size selection using Agencourt AMPure XP beads. .. A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA, USA).

Multiplexing:

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols. .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina).

Article Title: Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker
Article Snippet: Whole exome sequencing and data analysis Genomic DNA (1 μg) from the bone marrow and matching blood samples was sheared by Covaris S220 (Covaris, MA, USA) and used for library construction with SureSelect XT Human All Exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer's protocols. .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina, USA), using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Mutagenesis:

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: Paragraph title: Germline MMR gene mutation analysis ... A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA, USA).

Isolation:

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: Matching blood DNA was isolated by the QIAamp DNA blood kit (Qiagen). .. For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols.

Purification:

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: .. A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using a SureSelect XT Reagent kit (Agilent Technologies, Santa Clara, CA), Each library was synthesized with sample-specific barcodes of 6 bp, quantified using PicoGreen, and four libraries were pooled to a total of 600 ng for hybrid capture using an Agilent SureSelectXT custom kit (OPv2 RNA bait, 2.9 Mb; Agilent Technologies). .. The concentration of the enriched target was measured by quantitative polymerase chain reaction (PCR) (Kapa Biosystems, Woburn, MA), and loaded on the MiSeq platform (Illumina Inc., San Diego, CA) for paired end sequencing.

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: From the CD138− enriched cells, genomic DNA and RNA was purified using the AllPrep kit (Qiagen). .. For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols.

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: .. A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA, USA). ..

Article Title: Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers
Article Snippet: Genomic DNA was sheared using the Covaris S220 (Covaris, Woburn, MA) to construct a sequencing library using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) on target genes. .. A paired-end sequencing library was purified and amplified with a barcode tag, and the library quality and quantity were determined.

Article Title: Circulating tumor DNA shows variable clonal response of breast cancer during neoadjuvant chemotherapy
Article Snippet: The sequencing libraries for primary tumor tissue samples were created by using SureSelect XT reagent kit, HSQ (Agilent Technologies) following the manufacturer’s recommended protocols. .. DNA fragments were ligated with pre-indexed PentAdapter™ (PentaBase ApS, Denmark) at 4°C overnight, purified using AMPure XP beads (Beckman Coulter, Indianapolis, IN, USA), amplified with P5 and P7 oligonucleotides, and subjected to hybrid selection for target enrichment.

Sequencing:

Article Title: Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application
Article Snippet: Paragraph title: DNA library construction and high-throughput sequencing ... A DNA library was prepared as described in our previous report using the S1 method ; briefly, gDNA shearing with S1 enzyme, end repair, A-tailing, and ligation with the TruSeq adaptor using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA, USA).

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using a SureSelect XT Reagent kit (Agilent Technologies, Santa Clara, CA), Each library was synthesized with sample-specific barcodes of 6 bp, quantified using PicoGreen, and four libraries were pooled to a total of 600 ng for hybrid capture using an Agilent SureSelectXT custom kit (OPv2 RNA bait, 2.9 Mb; Agilent Technologies). .. The concentration of the enriched target was measured by quantitative polymerase chain reaction (PCR) (Kapa Biosystems, Woburn, MA), and loaded on the MiSeq platform (Illumina Inc., San Diego, CA) for paired end sequencing.

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols. .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina).

Article Title: Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker
Article Snippet: .. Whole exome sequencing and data analysis Genomic DNA (1 μg) from the bone marrow and matching blood samples was sheared by Covaris S220 (Covaris, MA, USA) and used for library construction with SureSelect XT Human All Exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer's protocols. .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina, USA), using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA, USA). .. The concentration of the enriched target was measured by quantitative PCR (Kapa Biosystems, Inc., Woburn, MA, USA), and samples were loaded onto the MiSeq platform for paired-end sequencing.

Article Title: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: Genomic DNA from 12 nodules and their corresponding cirrhotic tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of a library using SureSelect XT Human All Exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol. .. After the enriched exome libraries were multiplexed, the libraries were sequenced on HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA).

Article Title: Four distinct immune microenvironment subtypes in gastric adenocarcinoma with special reference to microsatellite instability
Article Snippet: .. Deep targeted sequencing of DNA Genomic DNA (250 ng) from FFPE tissue was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn, Massachusetts, USA) and used for library construction with SureSelect XT reagent kit, HSQ (Agilent Technologies, Santa Clara, California, USA) based on the manufacturer’s protocol. ..

Article Title: Clinical Relevance of Genomic Changes in Recurrent Pediatric Solid Tumors
Article Snippet: Paragraph title: Sequencing Using a Cancer Panel (CancerSCAN) ... Genomic DNA (250 ng) from each tissue was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn, MA) and used to construct a library using CancerSCAN , probes and a SureSelect XT reagent kit (HSQ; Agilent Technologies) according to the manufacturer's protocol.

Article Title: Novel MXD4–NUTM1 fusion transcript identified in primary ovarian undifferentiated small round cell sarcoma, et al. Novel MXD4–NUTM1 fusion transcript identified in primary ovarian undifferentiated small round cell sarcoma
Article Snippet: .. 2.3 Whole‐exome sequencing and analysis Two hundred nanograms of DNA from a patient with ovarian sarcoma and her normal blood sample were used for preparing sequencing libraries using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA). .. Target‐gene enrichment was conducted with SureSelect Human All Exon V5 + lncRNA Kit (Agilent Technologies).

Article Title: Clinical Relevance of Genomic Changes in Recurrent Pediatric Solid Tumors
Article Snippet: .. Sequencing Using a Cancer Panel (CancerSCAN) Genomic DNA (250 ng) from each tissue was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn, MA) and used to construct a library using CancerSCAN , probes and a SureSelect XT reagent kit (HSQ; Agilent Technologies) according to the manufacturer's protocol. ..

Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
Article Snippet: DNA library preparation was performed for each sample using the Agilent SureSelect XT Reagent Kit per the manufacturer’s protocol ( http://www.ogt.co.uk/assets/0000/4457/990162_HB_SureSeqSolidTumour_110215.pdf ). .. In-depth sequencing was performed to achieve a mean sequencing depth of 500 reads for all targeted coding bases.

Article Title: Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers
Article Snippet: .. Genomic DNA was sheared using the Covaris S220 (Covaris, Woburn, MA) to construct a sequencing library using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) on target genes. .. A paired-end sequencing library was purified and amplified with a barcode tag, and the library quality and quantity were determined.

Article Title: Circulating tumor DNA shows variable clonal response of breast cancer during neoadjuvant chemotherapy
Article Snippet: .. The sequencing libraries for primary tumor tissue samples were created by using SureSelect XT reagent kit, HSQ (Agilent Technologies) following the manufacturer’s recommended protocols. .. Sequencing libraries for PBL and plasma DNAs were constructed with KAPA Hyper Prep kits (Kapa Biosystems, Woburn, MA, USA) [ ].

Article Title: Novel MXD4–NUTM1 fusion transcript identified in primary ovarian undifferentiated small round cell sarcoma, et al. Novel MXD4–NUTM1 fusion transcript identified in primary ovarian undifferentiated small round cell sarcoma
Article Snippet: .. Two hundred nanograms of DNA from a patient with ovarian sarcoma and her normal blood sample were used for preparing sequencing libraries using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA). .. Target‐gene enrichment was conducted with SureSelect Human All Exon V5 + lncRNA Kit (Agilent Technologies).

Selection:

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: Targeted Next Generation Sequencing Targeted NGS was performed using the MiSeq platform (Illumina, San Diego, CA, USA) with OncoPanel version 2 (OPv2) for capturing exons of 505 cancer-related genes plus partial introns from 15 genes often rearranged in cancer . gDNA 200 ng was fragmented by sonication (Covaris Inc., Woburn, MA) to an average of 250 bp, followed by size selection using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, UK). .. A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using a SureSelect XT Reagent kit (Agilent Technologies, Santa Clara, CA), Each library was synthesized with sample-specific barcodes of 6 bp, quantified using PicoGreen, and four libraries were pooled to a total of 600 ng for hybrid capture using an Agilent SureSelectXT custom kit (OPv2 RNA bait, 2.9 Mb; Agilent Technologies).

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: Genomic DNA (200 ng) from normal small intestine mucosa was fragmented to 250 bp by sonication (Covaris Inc., Woburn, MA, USA), followed by size selection using Agencourt AMPure XP beads. .. A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA, USA).

Article Title: Circulating tumor DNA shows variable clonal response of breast cancer during neoadjuvant chemotherapy
Article Snippet: The sequencing libraries for primary tumor tissue samples were created by using SureSelect XT reagent kit, HSQ (Agilent Technologies) following the manufacturer’s recommended protocols. .. DNA fragments were ligated with pre-indexed PentAdapter™ (PentaBase ApS, Denmark) at 4°C overnight, purified using AMPure XP beads (Beckman Coulter, Indianapolis, IN, USA), amplified with P5 and P7 oligonucleotides, and subjected to hybrid selection for target enrichment.

Sample Prep:

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols. .. Sequencing libraries were generated and multiplexed using Nextera XT DNA sample prep kit (Illumina) and sequenced on the HiSeq 2500 in the 100-bp paired-end mode of the TruSeq rapid PE cluster kit and TruSeq rapid SBS kit following the Smart-seq2 protocol ( ).

Next-Generation Sequencing:

Article Title: Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application
Article Snippet: DNA library construction and high-throughput sequencing Targeted NGS was performed using MiSeq (Illumina, Inc., San Diego, CA, USA) with OncoPanel AMCv3 (OP-AMCv3, developed in-house by Asan-CCGD) to include the exons of 199 genes (575,147 bp) and partial introns from 8 genes often rearranged in cancer (209,397 bp) to detect fusion genes and additional small (10,534 bp) specific single nucleotide polymorphism loci for CNV analysis. .. A DNA library was prepared as described in our previous report using the S1 method ; briefly, gDNA shearing with S1 enzyme, end repair, A-tailing, and ligation with the TruSeq adaptor using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA, USA).

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: Paragraph title: Targeted Next Generation Sequencing ... A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using a SureSelect XT Reagent kit (Agilent Technologies, Santa Clara, CA), Each library was synthesized with sample-specific barcodes of 6 bp, quantified using PicoGreen, and four libraries were pooled to a total of 600 ng for hybrid capture using an Agilent SureSelectXT custom kit (OPv2 RNA bait, 2.9 Mb; Agilent Technologies).

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: Germline MMR gene mutation analysis Targeted next-generation sequencing was performed using the MiSeq platform (Illumina, Inc., San Diego, CA, USA) with OncoPanel_AMCv3 (OP_AMCv3, Celemics Inc., Seoul, Korea) to capture the exons of MLH1 , MSH2 , MSH6 , and PMS2 . .. A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA, USA).

Article Title: PI3K as a potential therapeutic target in thymic epithelial tumors
Article Snippet: Paragraph title: Next-Generation-Sequencing Library Construction ... MP57 samples and IU-TAB1 sheared DNA samples were constructed into individual libraries using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA) or the Personal Genome Diagnostics (PGDx) custom library kit (PGDx, Baltimore, MD), according to the manufacturers’ protocols.

Concentration Assay:

Article Title: Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application
Article Snippet: A DNA library was prepared as described in our previous report using the S1 method ; briefly, gDNA shearing with S1 enzyme, end repair, A-tailing, and ligation with the TruSeq adaptor using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA, USA). .. The concentration of the enriched target was measured using quantitative polymerase chain reaction (qPCR; Kapa Biosystems, Inc., Woburn, MA, USA).

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using a SureSelect XT Reagent kit (Agilent Technologies, Santa Clara, CA), Each library was synthesized with sample-specific barcodes of 6 bp, quantified using PicoGreen, and four libraries were pooled to a total of 600 ng for hybrid capture using an Agilent SureSelectXT custom kit (OPv2 RNA bait, 2.9 Mb; Agilent Technologies). .. The concentration of the enriched target was measured by quantitative polymerase chain reaction (PCR) (Kapa Biosystems, Woburn, MA), and loaded on the MiSeq platform (Illumina Inc., San Diego, CA) for paired end sequencing.

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA, USA). .. The concentration of the enriched target was measured by quantitative PCR (Kapa Biosystems, Inc., Woburn, MA, USA), and samples were loaded onto the MiSeq platform for paired-end sequencing.

High Throughput Screening Assay:

Article Title: Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application
Article Snippet: Paragraph title: DNA library construction and high-throughput sequencing ... A DNA library was prepared as described in our previous report using the S1 method ; briefly, gDNA shearing with S1 enzyme, end repair, A-tailing, and ligation with the TruSeq adaptor using the SureSelect XT reagent kit (Agilent Technologies, Santa Clara, CA, USA).

Staining:

Article Title: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: Genomic DNA preparation from FFPE tissues for WES Ten formalin fixed paraffin embedded (FFPE) sections of 10 μm from each lesion were stained with eosin. .. Genomic DNA from 12 nodules and their corresponding cirrhotic tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of a library using SureSelect XT Human All Exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol.

Variant Assay:

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: A DNA library was prepared by ligation of 50 ng of purified DNA with a TruSeq adaptor using the SureSelect XT Reagent Kit (Agilent Technologies, Santa Clara, CA, USA). .. The data were analyzed with a laboratory-developed pipeline for variant calling.

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    Agilent technologies sureselect xt reagent kit
    Sureselect Xt Reagent Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 95/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    sureselect xt reagent kit - by Bioz Stars, 2020-02
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