Structured Review

Agilent technologies sureselect xt reagent kit
Sureselect Xt Reagent Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 96/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/sureselect xt reagent kit/product/Agilent technologies
Average 96 stars, based on 12 article reviews
Price from $9.99 to $1999.99
sureselect xt reagent kit - by Bioz Stars, 2019-10
96/100 stars

Images

Related Articles

Multiplexing:

Article Title: Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients
Article Snippet: The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions. .. Briefly, after end repair and A-tailing according to the manufacturer’s protocol, we performed adaptor ligation at 4 °C overnight using a pre-indexed PentAdapter™ (PentaBase ApS, Denmark).

Amplification:

Article Title: Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing
Article Snippet: The gDNA library (750 ng) was prepared for hybridization with the capture beads, and the sample was hybridized for 24 h at 65°C, captured with the Dynabeads MyOne Streptavidin T1 (Thermo Fisher Scientific, Inc., Waltham, MA, USA) and purified using Agencourt AMPure XP beads. .. The Agilent protocol was used for addition of index tags (Agilent SureSelect XT Reagent kit; Illumina, Inc., San Diego, CA, USA; cat. no. G9611B) by post-hybridization amplification. .. Finally, all samples were sequenced on an Illumina Sequencer (Illumina, Inc., San Diego, CA, USA) using the 150PE protocol as specified by Illumina, Inc.

Article Title: Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers, et al. Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers
Article Snippet: Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below. .. Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below.

Article Title: Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers, et al. Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers
Article Snippet: 2.3 Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below. .. 2.3 Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below.

Article Title: Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing
Article Snippet: A total of 1 µg genomic DNA (gDNA) was used to construct a library with the Agilent SureSelect XT Reagent kit. .. A total of 1 µg genomic DNA (gDNA) was used to construct a library with the Agilent SureSelect XT Reagent kit.

Article Title: Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients
Article Snippet: The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions. .. Briefly, after end repair and A-tailing according to the manufacturer’s protocol, we performed adaptor ligation at 4 °C overnight using a pre-indexed PentAdapter™ (PentaBase ApS, Denmark).

Article Title: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: Exon 9 was amplified with the following primers: 5′-CTCCCTGTTGGTGATGAGGT-3′ (forward) and 5′-GGGTCCTTCTCCCAGCTCTA-3′ (reverse). .. A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark).

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. .. 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.

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: Targeting the Golgi apparatus to overcome acquired resistance of non-small cell lung cancer cells to EGFR tyrosine kinase inhibitors
Article Snippet: Briefly, the genomic library was prepared from randomly cleaved gDNA fragments by use of an Acoustic Solubilizer (Covaris, Inc., Woburn, MA). .. Then, the fragments were PCR amplified to create sequencing libraries by using SureSelect XT reagent Kit and SureSelect Human ALL Exon Kit V5 (Agilent Technologies, Santa Clara, CA). .. NGS was performed by use of HiSeq 2500 (Illumina Inc., San Diego, CA).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Genomic DNA (1 μg) from each sample was sheared using the Covaris S220 (Covaris, Woburn, MA) and used to construct a library using SureSelect XT Human All Exon V5 and a SureSelect XT Reagent Kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Genomic DNA (1 μg) from each sample was sheared using the Covaris S220 (Covaris, Woburn, MA) and used to construct a library using SureSelect XT Human All Exon V5 and a SureSelect XT Reagent Kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol.

Synthesized:

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: 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). .. 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.

Picogreen Assay:

Article Title: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: After the beads were dried for 5 min, DNA was eluted in 50 μL DNase-/RNase-free water, followed by quantification using the Quant-iT™ PicoGreen dsDNA Assay kit (Invitrogen Life Technologies). .. A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark).

Construct:

Article Title: Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing
Article Snippet: A total of 1 µg genomic DNA (gDNA) was used to construct a library with the Agilent SureSelect XT Reagent kit. .. The Agilent protocol was used for addition of index tags (Agilent SureSelect XT Reagent kit; Illumina, Inc., San Diego, CA, USA; cat. no. G9611B) by post-hybridization amplification.

Article Title: Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing
Article Snippet: In all cases, the SureSelect XT Human All Exon Version 6 (60 Mb) probe set (Agilent Technologies, Inc.) was used. .. A total of 1 µg genomic DNA (gDNA) was used to construct a library with the Agilent SureSelect XT Reagent kit. .. The amplification adapter-ligated sample was purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) and analyzed on a TapeStation 4200 D1000 screen tape (Agilent Technologies, Inc.).

Article Title: Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients
Article Snippet: Purified genomic DNA was sonicated (7 min, 0.5% duty, intensity of 0.1, and 50 cycles/burst) into 150–200 bp fragments using a Covaris S2 (Covaris Inc. Woburn, MA, USA). .. The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions. .. The PBL and plasma DNA libraries were created using a KAPA Hyper Prep Kit (Kapa Biosystems, Woburn, MA, USA) as described previously , .

Article Title: Prevalence and detection of low-allele-fraction variants in clinical cancer samples
Article Snippet: Genomic DNA was sheared using a Covaris S220 (Covaris, Woburn, MA). .. Target capture was performed using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) and a paired-end sequencing library was constructed with a barcode. .. After checking for library quality, sequencing was performed on a HiSeq 2500 with 100-bp reads (Illumina, San Diego, CA, USA).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: For RNA, concentration and purity were measured using the NanoDrop and Bioanalyzer (Agilent Technologies). .. Genomic DNA (1 μg) from each sample was sheared using the Covaris S220 (Covaris, Woburn, MA) and used to construct a library using SureSelect XT Human All Exon V5 and a SureSelect XT Reagent Kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. This kit is designed to enrich 335,756 exons of 21,058 genes, covering ~71 Mb of the human genome.

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). .. 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: Prevalence and detection of low-allele-fraction variants in clinical cancer samples
Article Snippet: The degree of DNA degradation was measured using a 200 TapeStation Instrument (Agilent Technologies, Santa Clara, CA, USA) and real-time PCR (Agilent Technologies). .. Target capture was performed using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) and a paired-end sequencing library was constructed with a barcode.

Article Title: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark). .. Each library was constructed with 6 bp sample-specific barcodes, quantified using PicoGreen, and four l ibraries were pooled to a total of 600 ng for hybrid capture using the Agilent SureSelectXT custom kit (OP_v2 RNA bait, 2.9 Mb; Agilent Technologies).

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). .. 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).

Formalin-fixed Paraffin-Embedded:

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 ( ).

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 ).

Article Title: Prevalence and detection of low-allele-fraction variants in clinical cancer samples
Article Snippet: Genomic DNA was extracted from fresh tissues using QIAamp DNA mini kits (Qiagen, Valencia, CA, USA) and from FFPE tissues using either a Promega Maxwell 16 CSC DNA FFPE kit or a QIAamp DNA FFPE Tissue kit. .. Target capture was performed using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) and a paired-end sequencing library was constructed with a barcode.

Article Title: Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile
Article Snippet: The QIAamp DNA FFPE Tissue kit (Qiagen) was used to extract DNA from FFPE tissues. .. Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below.

Activity Assay:

Article Title: Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile
Article Snippet: Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below. .. Sheared DNA was purified using QIAquick PCR Purification kit (Qiagen).

Hybridization:

Article Title: Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing
Article Snippet: The gDNA library (750 ng) was prepared for hybridization with the capture beads, and the sample was hybridized for 24 h at 65°C, captured with the Dynabeads MyOne Streptavidin T1 (Thermo Fisher Scientific, Inc., Waltham, MA, USA) and purified using Agencourt AMPure XP beads. .. The Agilent protocol was used for addition of index tags (Agilent SureSelect XT Reagent kit; Illumina, Inc., San Diego, CA, USA; cat. no. G9611B) by post-hybridization amplification.

Article Title: Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing
Article Snippet: A total of 1 µg genomic DNA (gDNA) was used to construct a library with the Agilent SureSelect XT Reagent kit. .. The amplification adapter-ligated sample was purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) and analyzed on a TapeStation 4200 D1000 screen tape (Agilent Technologies, Inc.).

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. .. For hybrid selection, we designed unique RNA baits that targeted ∼202 kb of the human genome, including exons from 82 cancer-related genes ( ).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Genomic DNA (1 μg) from each sample was sheared using the Covaris S220 (Covaris, Woburn, MA) and used to construct a library using SureSelect XT Human All Exon V5 and a SureSelect XT Reagent Kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Briefly, a paired-end DNA sequencing library was prepared by gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

Ligation:

Article Title: Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application
Article Snippet: 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). .. Each library was constructed with sample-specific barcodes 6 bp in size and quantified using the Qubit kit.

Article Title: Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers, et al. Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers
Article Snippet: Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below. .. Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below.

Article Title: Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers, et al. Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers
Article Snippet: 2.3 Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below. .. 2.3 Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below.

Article Title: Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients
Article Snippet: The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions. .. When constructing the sequencing libraries, 200 ng of PBL DNA and 37.12 ng of plasma DNA were used on average.

Article Title: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: Samples (200 ng) of gDNA were fragmented by sonication (Covaris Inc., Woburn, MA) to an average size of 250 bp, followed by size selection using Agencourt AMPure XP beads (Beckman Coulter, Inc., Fullerton, CA). .. A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark). .. Each library was constructed with 6 bp sample-specific barcodes, quantified using PicoGreen, and four l ibraries were pooled to a total of 600 ng for hybrid capture using the Agilent SureSelectXT custom kit (OP_v2 RNA bait, 2.9 Mb; Agilent Technologies).

Article Title: Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile
Article Snippet: Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below. .. Using a combination of enzymes with filling and exonuclease activity, the DNA fragments became blunt ended.

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). .. Each library was made with sample-specific barcodes 6 bp in size and quantified using PicoGreen, and eight libraries were pooled to a total of 700 ng for hybrid capture using an OP_AMCv3 RNA bait.

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: 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). .. 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: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Genomic DNA (1 μg) from each sample was sheared using the Covaris S220 (Covaris, Woburn, MA) and used to construct a library using SureSelect XT Human All Exon V5 and a SureSelect XT Reagent Kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. After enriched exome libraries were multiplexed, the libraries were sequenced using a HiSeq 2500 sequencing platform (Illumina, San Diego, CA).

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. .. 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).

DNA Sequencing:

Article Title: Targeting the Golgi apparatus to overcome acquired resistance of non-small cell lung cancer cells to EGFR tyrosine kinase inhibitors
Article Snippet: Paragraph title: DNA sequencing and allele quantification assay ... Then, the fragments were PCR amplified to create sequencing libraries by using SureSelect XT reagent Kit and SureSelect Human ALL Exon Kit V5 (Agilent Technologies, Santa Clara, CA).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Genomic DNA (1 μg) from each sample was sheared using the Covaris S220 (Covaris, Woburn, MA) and used to construct a library using SureSelect XT Human All Exon V5 and a SureSelect XT Reagent Kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. After enriched exome libraries were multiplexed, the libraries were sequenced using a HiSeq 2500 sequencing platform (Illumina, San Diego, CA).

Polymerase Chain Reaction:

Article Title: Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers, et al. Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers
Article Snippet: Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below. .. Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below.

Article Title: Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers, et al. Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers
Article Snippet: 2.3 Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below. .. 2.3 Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below.

Article Title: Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients
Article Snippet: The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions. .. Briefly, after end repair and A-tailing according to the manufacturer’s protocol, we performed adaptor ligation at 4 °C overnight using a pre-indexed PentAdapter™ (PentaBase ApS, Denmark).

Article Title: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: The Sanger sequencing of all PCR products was subsequently conducted on an ABI Prism 3730xl Genetic Analyzer (Life Technologies, Carlsbad, CA). .. A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark).

Article Title: Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile
Article Snippet: Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below. .. Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below.

Article Title: Targeting the Golgi apparatus to overcome acquired resistance of non-small cell lung cancer cells to EGFR tyrosine kinase inhibitors
Article Snippet: Briefly, the genomic library was prepared from randomly cleaved gDNA fragments by use of an Acoustic Solubilizer (Covaris, Inc., Woburn, MA). .. Then, the fragments were PCR amplified to create sequencing libraries by using SureSelect XT reagent Kit and SureSelect Human ALL Exon Kit V5 (Agilent Technologies, Santa Clara, CA). .. NGS was performed by use of HiSeq 2500 (Illumina Inc., San Diego, CA).

Sonication:

Article Title: Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients
Article Snippet: Purified genomic DNA was sonicated (7 min, 0.5% duty, intensity of 0.1, and 50 cycles/burst) into 150–200 bp fragments using a Covaris S2 (Covaris Inc. Woburn, MA, USA). .. The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions.

Article Title: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: Samples (200 ng) of gDNA were fragmented by sonication (Covaris Inc., Woburn, MA) to an average size of 250 bp, followed by size selection using Agencourt AMPure XP beads (Beckman Coulter, Inc., Fullerton, CA). .. A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark).

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: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: 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).

DNA Extraction:

Article Title: Prevalence and detection of low-allele-fraction variants in clinical cancer samples
Article Snippet: Paragraph title: DNA extraction and library preparation and sequencing ... Target capture was performed using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) and a paired-end sequencing library was constructed with a barcode.

Mutagenesis:

Article Title: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: For additional validation of P286R mutation and overall mutation burden, targeted next-generation sequencing was performed using the MiSeq platform (Illumina), with OncoPanel version 2 (OP_v2) (Agilent, custom-ordered), to capture the exons of 505 cancer-related genes plus partial introns from 15 genes often rearranged in cancer. .. A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark).

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: Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile
Article Snippet: The characterized biopsies were subjected to sample isolation from the affected areas of the blocks using 1mm diameter disposable biopsy punches (Miltex). .. Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below.

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: Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing
Article Snippet: The gDNA library (750 ng) was prepared for hybridization with the capture beads, and the sample was hybridized for 24 h at 65°C, captured with the Dynabeads MyOne Streptavidin T1 (Thermo Fisher Scientific, Inc., Waltham, MA, USA) and purified using Agencourt AMPure XP beads. .. The Agilent protocol was used for addition of index tags (Agilent SureSelect XT Reagent kit; Illumina, Inc., San Diego, CA, USA; cat. no. G9611B) by post-hybridization amplification.

Article Title: Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers, et al. Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers
Article Snippet: Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below. .. Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below.

Article Title: Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers, et al. Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers
Article Snippet: 2.3 Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below. .. 2.3 Library construction was performed on the 54 DNA samples (18 sets of carcinoma, adenoma, normal triplets) using Agilent Technologies SureSelect XT Reagent Kit, HSQ (cat # G9611A) as described below.

Article Title: Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing
Article Snippet: A total of 1 µg genomic DNA (gDNA) was used to construct a library with the Agilent SureSelect XT Reagent kit. .. The amplification adapter-ligated sample was purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) and analyzed on a TapeStation 4200 D1000 screen tape (Agilent Technologies, Inc.).

Article Title: Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients
Article Snippet: Purified genomic DNA was sonicated (7 min, 0.5% duty, intensity of 0.1, and 50 cycles/burst) into 150–200 bp fragments using a Covaris S2 (Covaris Inc. Woburn, MA, USA). .. The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions.

Article Title: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: Samples (200 ng) of gDNA were fragmented by sonication (Covaris Inc., Woburn, MA) to an average size of 250 bp, followed by size selection using Agencourt AMPure XP beads (Beckman Coulter, Inc., Fullerton, CA). .. A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark). .. Each library was constructed with 6 bp sample-specific barcodes, quantified using PicoGreen, and four l ibraries were pooled to a total of 600 ng for hybrid capture using the Agilent SureSelectXT custom kit (OP_v2 RNA bait, 2.9 Mb; Agilent Technologies).

Article Title: Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile
Article Snippet: Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below. .. Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below.

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. .. 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.

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). .. Each library was made with sample-specific barcodes 6 bp in size and quantified using PicoGreen, and eight libraries were pooled to a total of 700 ng for hybrid capture using an OP_AMCv3 RNA bait.

Article Title: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: 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). .. 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: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Genomic DNA (1 μg) from each sample was sheared using the Covaris S220 (Covaris, Woburn, MA) and used to construct a library using SureSelect XT Human All Exon V5 and a SureSelect XT Reagent Kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Briefly, a paired-end DNA sequencing library was prepared by gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

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: Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing
Article Snippet: Paragraph title: Library preparation and sequencing ... The Agilent protocol was used for addition of index tags (Agilent SureSelect XT Reagent kit; Illumina, Inc., San Diego, CA, USA; cat. no. G9611B) by post-hybridization amplification.

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 ( ). .. DNA library preparation was performed for each sample using the Agilent SureSelect XT Reagent Kit per 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 ). .. 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 ).

Article Title: Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients
Article Snippet: The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions. .. The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions.

Article Title: Prevalence and detection of low-allele-fraction variants in clinical cancer samples
Article Snippet: Genomic DNA was sheared using a Covaris S220 (Covaris, Woburn, MA). .. Target capture was performed using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) and a paired-end sequencing library was constructed with a barcode. .. After checking for library quality, sequencing was performed on a HiSeq 2500 with 100-bp reads (Illumina, San Diego, CA, USA).

Article Title: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: Paragraph title: Targeted sequencing ... A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark).

Article Title: Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile
Article Snippet: DNeasy Blood & Tissue kit (Qiagen) was used to extract DNA from blood samples. .. Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below. .. Briefly, 1–3 μg genomic DNA was sheared using Covaris S2 Focused-ultrasonicator, in a 130 μl volume, with 5.0 intensity, 10% duty cycle, 200 cycles per burst, and 6:00 minutes treatment time.

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: Frozen tumor and matched normal blood samples were obtained at the Niigata University Medical and Dental Hospital. .. 2.3 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: Circulating tumor DNA shows variable clonal response of breast cancer during neoadjuvant chemotherapy
Article Snippet: Plasma DNA was used for library construction without fragmentation. .. 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: 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). .. 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: 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 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: Targeting the Golgi apparatus to overcome acquired resistance of non-small cell lung cancer cells to EGFR tyrosine kinase inhibitors
Article Snippet: Briefly, the genomic library was prepared from randomly cleaved gDNA fragments by use of an Acoustic Solubilizer (Covaris, Inc., Woburn, MA). .. Then, the fragments were PCR amplified to create sequencing libraries by using SureSelect XT reagent Kit and SureSelect Human ALL Exon Kit V5 (Agilent Technologies, Santa Clara, CA). .. NGS was performed by use of HiSeq 2500 (Illumina Inc., San Diego, CA).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Paragraph title: Whole-Exome Sequencing ... Genomic DNA (1 μg) from each sample was sheared using the Covaris S220 (Covaris, Woburn, MA) and used to construct a library using SureSelect XT Human All Exon V5 and a SureSelect XT Reagent Kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol.

Blocking Assay:

Article Title: Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile
Article Snippet: Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below. .. Using a combination of enzymes with filling and exonuclease activity, the DNA fragments became blunt ended.

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. .. For hybrid selection, we designed unique RNA baits that targeted ∼202 kb of the human genome, including exons from 82 cancer-related genes ( ).

Multiplex Assay:

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. .. For hybrid selection, we designed unique RNA baits that targeted ∼202 kb of the human genome, including exons from 82 cancer-related genes ( ).

Selection:

Article Title: Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients
Article Snippet: The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions. .. The FNA sample libraries were constructed using the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s instructions.

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. .. 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.

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: Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS
Article Snippet: 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).

Sample Prep:

Article Title: Prevalence and detection of low-allele-fraction variants in clinical cancer samples
Article Snippet: Target capture was performed using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) and a paired-end sequencing library was constructed with a barcode. .. After checking for library quality, sequencing was performed on a HiSeq 2500 with 100-bp reads (Illumina, San Diego, CA, USA).

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).

Next-Generation Sequencing:

Article Title: Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application
Article Snippet: 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: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: For additional validation of P286R mutation and overall mutation burden, targeted next-generation sequencing was performed using the MiSeq platform (Illumina), with OncoPanel version 2 (OP_v2) (Agilent, custom-ordered), to capture the exons of 505 cancer-related genes plus partial introns from 15 genes often rearranged in cancer. .. A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark).

Article Title: Lynch syndrome-related small intestinal adenocarcinomas
Article Snippet: 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: 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: Targeting the Golgi apparatus to overcome acquired resistance of non-small cell lung cancer cells to EGFR tyrosine kinase inhibitors
Article Snippet: Preparation of sequence libraries and analysis of the next generation DNA sequencing (NGS) were conducted by Takara Bio Inc., (Shiga, Japan). .. Then, the fragments were PCR amplified to create sequencing libraries by using SureSelect XT reagent Kit and SureSelect Human ALL Exon Kit V5 (Agilent Technologies, Santa Clara, CA).

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). .. 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: Prevalence and detection of low-allele-fraction variants in clinical cancer samples
Article Snippet: DNA concentration and purity were checked using a Nanodrop 8000 UV-Vis spectrometer (Thermo Scientific, Waltham, MA, USA) and Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY, USA). .. Target capture was performed using the SureSelect XT Reagent Kit, HSQ (Agilent Technologies) and a paired-end sequencing library was constructed with a barcode.

Article Title: The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy
Article Snippet: A DNA library was prepared by ligation of 50 ng purified DNA with the TruSeq adaptor using a SureSelect XT Reagent Kit (Agilent Technologies, Glostrup, Denmark). .. Each library was constructed with 6 bp sample-specific barcodes, quantified using PicoGreen, and four l ibraries were pooled to a total of 600 ng for hybrid capture using the Agilent SureSelectXT custom kit (OP_v2 RNA bait, 2.9 Mb; Agilent Technologies).

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). .. 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).

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).

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 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.

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Agilent technologies sureselect xt
    Coverage distribution across 90 PCR-capture amplicons between FF and FFPE samples. Coverage distribution across the 90 ‘AmpliSeq Colon and Lung Cancer Panel’ regions displays a similar trend between the FF (blue) and FFPE (red) libraries in both Agilent <t>SureSelect</t> ( a ) and Roche NimbleGen ( b ) libraries respectively, with a slightly better coverage in FFPE samples. Each amplicon is identified by a number as reported in Additional file 3 : TableS7
    Sureselect Xt, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselect xt/product/Agilent technologies
    Average 99 stars, based on 17 article reviews
    Price from $9.99 to $1999.99
    sureselect xt - by Bioz Stars, 2019-10
    99/100 stars
      Buy from Supplier

    96
    Agilent technologies sureselect xt reagent kit
    Coverage distribution across 90 PCR-capture amplicons between FF and FFPE samples. Coverage distribution across the 90 ‘AmpliSeq Colon and Lung Cancer Panel’ regions displays a similar trend between the FF (blue) and FFPE (red) libraries in both Agilent <t>SureSelect</t> ( a ) and Roche NimbleGen ( b ) libraries respectively, with a slightly better coverage in FFPE samples. Each amplicon is identified by a number as reported in Additional file 3 : TableS7
    Sureselect Xt Reagent Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 96/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselect xt reagent kit/product/Agilent technologies
    Average 96 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
    sureselect xt reagent kit - by Bioz Stars, 2019-10
    96/100 stars
      Buy from Supplier

    Image Search Results


    Coverage distribution across 90 PCR-capture amplicons between FF and FFPE samples. Coverage distribution across the 90 ‘AmpliSeq Colon and Lung Cancer Panel’ regions displays a similar trend between the FF (blue) and FFPE (red) libraries in both Agilent SureSelect ( a ) and Roche NimbleGen ( b ) libraries respectively, with a slightly better coverage in FFPE samples. Each amplicon is identified by a number as reported in Additional file 3 : TableS7

    Journal: BMC Cancer

    Article Title: Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

    doi: 10.1186/s12885-016-2720-4

    Figure Lengend Snippet: Coverage distribution across 90 PCR-capture amplicons between FF and FFPE samples. Coverage distribution across the 90 ‘AmpliSeq Colon and Lung Cancer Panel’ regions displays a similar trend between the FF (blue) and FFPE (red) libraries in both Agilent SureSelect ( a ) and Roche NimbleGen ( b ) libraries respectively, with a slightly better coverage in FFPE samples. Each amplicon is identified by a number as reported in Additional file 3 : TableS7

    Article Snippet: Here we present a comprehensive comparison of the Roche NimbleGen SeqCap EZ Exome (v .3.0; 64 Mb) and Agilent SureSelect XT (v .5; 50 Mb) (Table ), on genomic DNA (gDNA) extracted from FF and matched FFPE tissue belonging to five lung adenocarcinoma (ADC) patients.

    Techniques: Polymerase Chain Reaction, Formalin-fixed Paraffin-Embedded, Amplification

    Coverage distribution across all the coding exons of 623 cancer-related genes in both WES platforms. Distribution summary of 623 cancer-related genes according to their coverage performance achieved in the two tested WES systems ( a ). Specifically, 36 % of the genes (red) were completely well covered by both Agilent and Roche kits; 29 % (blue) had at least one ‘critical’ region in both kits; 18 % were completely well covered by Roche NimbleGen kit, but had one or more ‘critical’ region in Agilent SureSelect kit; finally, 17 % of the genes were completely well covered by Agilent SureSelect kit, but had one or more problematic region in Roche NimbleGen kit. Distribution summary of cancer-related genes having one (73 %), two (12 %) or more (15 %) critical regions in NimbleGen Roche kit, but completely well-covered in Agilent SureSelect kit ( b ). Distribution summary of cancer-related genes having one (66 %), two (25 %) or more (9 %) critical regions in Agilent SureSelect kit, but completely well-covered in Roche NimbleGen kit ( c )

    Journal: BMC Cancer

    Article Title: Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

    doi: 10.1186/s12885-016-2720-4

    Figure Lengend Snippet: Coverage distribution across all the coding exons of 623 cancer-related genes in both WES platforms. Distribution summary of 623 cancer-related genes according to their coverage performance achieved in the two tested WES systems ( a ). Specifically, 36 % of the genes (red) were completely well covered by both Agilent and Roche kits; 29 % (blue) had at least one ‘critical’ region in both kits; 18 % were completely well covered by Roche NimbleGen kit, but had one or more ‘critical’ region in Agilent SureSelect kit; finally, 17 % of the genes were completely well covered by Agilent SureSelect kit, but had one or more problematic region in Roche NimbleGen kit. Distribution summary of cancer-related genes having one (73 %), two (12 %) or more (15 %) critical regions in NimbleGen Roche kit, but completely well-covered in Agilent SureSelect kit ( b ). Distribution summary of cancer-related genes having one (66 %), two (25 %) or more (9 %) critical regions in Agilent SureSelect kit, but completely well-covered in Roche NimbleGen kit ( c )

    Article Snippet: Here we present a comprehensive comparison of the Roche NimbleGen SeqCap EZ Exome (v .3.0; 64 Mb) and Agilent SureSelect XT (v .5; 50 Mb) (Table ), on genomic DNA (gDNA) extracted from FF and matched FFPE tissue belonging to five lung adenocarcinoma (ADC) patients.

    Techniques:

    Variant calling comparison between Ion PGM data and both WES systems. Variant calling comparison between Ion PGM data (blue) and both Agilent SureSelect (green) and Roche NimbleGen (red) data in exon regions shows 88 % of concordance (44/50) in both WES capture systems ( a ). Both systems failed to call 4 genetic variants (*) detected by Ion PGM platform at low frequencies (4-16 %). Further 4 variants were missed as follows: 2 by Agilent (COSM6225, rs80338963) and 2 by Roche NimbleGen (COSM40942, rs35775721). Horizontal axis reports the genetic variants (Additional file 3 : Table S8a) ordered from lowest to highest frequency (vertical axis) as assessed by Ion PGM platform. Variant coverage displays a quite similar trend between Agilent (green) and Roche NimbleGen (red) libraries, and is far lower than Ion PGM platform (blue) ( b ). Two Roche libraries report a low coverage in the uncalled variants (COSM40942, rs35775721). Vertical axis displays the variant coverage in logarithmic scale. Variant calling comparison between Ion PGM data (blue) and both Agilent (green) and Roche NimbleGen (red) data in non-exon regions shows a poor performance of both WES technologies ( c ). Both WES systems failed to call the rs839541 (*) SNP in ERBB4 gene, whereas rs1558544 SNP in EGFR was missed by all 10 Agilent libraries. Vertical axis reports the frequency of the genetic variants. Variant coverage comparison between Ion PGM data (blue) and both Agilent (green) and Roche NimbleGen (red) data in non-exon (intron/downstream/upstream) regions reports a low coverage in both exome capture kits ( d ); rs839541 SNP was completely uncovered in Agilent libraries. Vertical axis displays coverage values in logarithmic scale

    Journal: BMC Cancer

    Article Title: Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

    doi: 10.1186/s12885-016-2720-4

    Figure Lengend Snippet: Variant calling comparison between Ion PGM data and both WES systems. Variant calling comparison between Ion PGM data (blue) and both Agilent SureSelect (green) and Roche NimbleGen (red) data in exon regions shows 88 % of concordance (44/50) in both WES capture systems ( a ). Both systems failed to call 4 genetic variants (*) detected by Ion PGM platform at low frequencies (4-16 %). Further 4 variants were missed as follows: 2 by Agilent (COSM6225, rs80338963) and 2 by Roche NimbleGen (COSM40942, rs35775721). Horizontal axis reports the genetic variants (Additional file 3 : Table S8a) ordered from lowest to highest frequency (vertical axis) as assessed by Ion PGM platform. Variant coverage displays a quite similar trend between Agilent (green) and Roche NimbleGen (red) libraries, and is far lower than Ion PGM platform (blue) ( b ). Two Roche libraries report a low coverage in the uncalled variants (COSM40942, rs35775721). Vertical axis displays the variant coverage in logarithmic scale. Variant calling comparison between Ion PGM data (blue) and both Agilent (green) and Roche NimbleGen (red) data in non-exon regions shows a poor performance of both WES technologies ( c ). Both WES systems failed to call the rs839541 (*) SNP in ERBB4 gene, whereas rs1558544 SNP in EGFR was missed by all 10 Agilent libraries. Vertical axis reports the frequency of the genetic variants. Variant coverage comparison between Ion PGM data (blue) and both Agilent (green) and Roche NimbleGen (red) data in non-exon (intron/downstream/upstream) regions reports a low coverage in both exome capture kits ( d ); rs839541 SNP was completely uncovered in Agilent libraries. Vertical axis displays coverage values in logarithmic scale

    Article Snippet: Here we present a comprehensive comparison of the Roche NimbleGen SeqCap EZ Exome (v .3.0; 64 Mb) and Agilent SureSelect XT (v .5; 50 Mb) (Table ), on genomic DNA (gDNA) extracted from FF and matched FFPE tissue belonging to five lung adenocarcinoma (ADC) patients.

    Techniques: Variant Assay

    Variant calling comparison between Agilent SureSelect and Roche NimbleGen kit. Mean percentage ± SD of SNVs and InDels common to both library prep kits (blue), and private to either Roche (red) or Agilent (green) kit in both FF and FFPE samples. The average percentage of common SNVs ( a ) and InDels ( b ) was approximately 48 % (FF: 47.8 %; FFPE: 48.5 %) and 24 % (FF: 24 %; FFPE: 23.5 %) across the whole target region specific for each kit. The average percentage of common SNVs ( c ) and InDels ( d ) was approximately 92 % (FF: 91.9 %; FFPE: 93 %) and 69 % (FF: 69.7 %; FFPE: 69.1 %) across the 42 Mb target region shared between the two kits

    Journal: BMC Cancer

    Article Title: Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

    doi: 10.1186/s12885-016-2720-4

    Figure Lengend Snippet: Variant calling comparison between Agilent SureSelect and Roche NimbleGen kit. Mean percentage ± SD of SNVs and InDels common to both library prep kits (blue), and private to either Roche (red) or Agilent (green) kit in both FF and FFPE samples. The average percentage of common SNVs ( a ) and InDels ( b ) was approximately 48 % (FF: 47.8 %; FFPE: 48.5 %) and 24 % (FF: 24 %; FFPE: 23.5 %) across the whole target region specific for each kit. The average percentage of common SNVs ( c ) and InDels ( d ) was approximately 92 % (FF: 91.9 %; FFPE: 93 %) and 69 % (FF: 69.7 %; FFPE: 69.1 %) across the 42 Mb target region shared between the two kits

    Article Snippet: Here we present a comprehensive comparison of the Roche NimbleGen SeqCap EZ Exome (v .3.0; 64 Mb) and Agilent SureSelect XT (v .5; 50 Mb) (Table ), on genomic DNA (gDNA) extracted from FF and matched FFPE tissue belonging to five lung adenocarcinoma (ADC) patients.

    Techniques: Variant Assay, Formalin-fixed Paraffin-Embedded