Structured Review

Agilent technologies hsq
Hsq, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/hsq/product/Agilent technologies
Average 99 stars, based on 8 article reviews
Price from $9.99 to $1999.99
hsq - by Bioz Stars, 2019-10
99/100 stars

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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: Intratumor heterogeneity inferred from targeted deep sequencing as a prognostic indicator
Article Snippet: In brief, the cancer panel sequencing data were generated by DNA shearing, library construction, and sequencing on a HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA) according to manufacturer’s protocol. .. Libraries were constructed by end repair, A-tailing, paired-end adaptor ligation, amplification, hybridization, indexing, and enrichment using a SureSelectXT reagent kit, HSQ (Agilent Technologies). .. The sequencing reactions were performed with the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (lllumina).

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: 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: 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.

Article Title: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: Genomic DNA (250 ng) from the tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of the library using customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies), according to the manufacturer’s protocol. .. Genomic DNA (250 ng) from the tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of the library using customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies), according to the manufacturer’s protocol.

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. .. 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: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
Article Snippet: Genomic DNA (250 ng) from each tissue was sheared with Covaris S220 (Covaris, Woburn, MA, USA) and was used for the construction of a library using probes and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol. .. Genomic DNA (250 ng) from each tissue was sheared with Covaris S220 (Covaris, Woburn, MA, USA) and was used for the construction of a library using probes and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol.

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: Genomic DNA (1 µg) from each FFPE sample was sheared by Covaris S220 (Covaris, MA, USA) and used for construction of a library with SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Genomic DNA (1 µg) from each FFPE sample was sheared by Covaris S220 (Covaris, MA, USA) and used for construction of a library with SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol.

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Genomic DNA (1 μg) from each tissue sample was sheared using a Covaris S220 (Covaris, MA, USA) and used for the construction of a library using the SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Genomic DNA (1 μg) from each tissue sample was sheared using a Covaris S220 (Covaris, MA, USA) and used for the construction of a library using the SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol.

Article Title: Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences
Article Snippet: Next, the multiplexed barcoded libraries were enriched by clonal amplification using emulsion polymerase chain reaction (PCR) on Ion Sphere Particles (Ion PGMTemplate 200 Kit) and loaded on an Ion 316 Chip. .. For Illumina HiSeq 2500, we used 250 ng of gDNA after shearing DNA with the Covaris S220 (Covaris, Woburn, MA, USA) and constructed library with customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies) as previously described [ ].

Construct:

Article Title: Intratumor heterogeneity inferred from targeted deep sequencing as a prognostic indicator
Article Snippet: In brief, the cancer panel sequencing data were generated by DNA shearing, library construction, and sequencing on a HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA) according to manufacturer’s protocol. .. Libraries were constructed by end repair, A-tailing, paired-end adaptor ligation, amplification, hybridization, indexing, and enrichment using a SureSelectXT reagent kit, HSQ (Agilent Technologies). .. The sequencing reactions were performed with the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (lllumina).

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: Landscape of Actionable Genetic Alterations Profiled from 1,071 Tumor Samples in Korean Cancer Patients
Article Snippet: Genomic DNA was sheared using a Covaris S220 (Covaris, Woburn, MA). .. Target capture was performed using the Sure-Select XT Reagent Kit, HSQ (Agilent Technologies) and a paired-end sequencing library was constructed with a barcode. .. Sequencing was performed on a HiSeq 2500 with 100-bp reads (Illumina, San Diego, CA).

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.

Article Title: Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences
Article Snippet: Massively parallel sequencing was carried out on an Ion PGM using the Ion PGM Sequencing 200 Kit v2. .. For Illumina HiSeq 2500, we used 250 ng of gDNA after shearing DNA with the Covaris S220 (Covaris, Woburn, MA, USA) and constructed library with customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies) as previously described [ ]. .. After the library was hybridized with bait sequences for 16 hours, the captured library was purified and then amplified with an index barcode tag.

Real-time Polymerase Chain Reaction:

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.

Formalin-fixed Paraffin-Embedded:

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: Four distinct immune microenvironment subtypes in gastric adenocarcinoma with special reference to microsatellite instability
Article Snippet: To reduce interobserver variation, all cases were reviewed by the two pathologists, and in cases of disagreement, the final interpretation was determined by consensus using a multihead microscope. .. 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. .. This panel is designed to enrich exons of 381 cancer-related genes.

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: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: To improve sequencing quality, we used strict sample quality thresholds for extracted DNA: 1) purity: 260/280 > 1.8, 260/230 > 1.8; 2) total amount > 250 ng; and 3) degradation: ΔCt value < 2.0 or DNA median size > 0.35 kb. .. Genomic DNA (1 µg) from each FFPE sample was sheared by Covaris S220 (Covaris, MA, USA) and used for construction of a library with SureSelect XT Human All Exon v5 and the 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.

Hybridization:

Article Title: Intratumor heterogeneity inferred from targeted deep sequencing as a prognostic indicator
Article Snippet: In brief, the cancer panel sequencing data were generated by DNA shearing, library construction, and sequencing on a HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA) according to manufacturer’s protocol. .. Libraries were constructed by end repair, A-tailing, paired-end adaptor ligation, amplification, hybridization, indexing, and enrichment using a SureSelectXT reagent kit, HSQ (Agilent Technologies). .. The sequencing reactions were performed with the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (lllumina).

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.

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: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
Article Snippet: Genomic DNA (250 ng) from each tissue was sheared with Covaris S220 (Covaris, Woburn, MA, USA) and was used for the construction of a library using probes and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol. .. Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: Genomic DNA (1 µg) from each FFPE sample was sheared by Covaris S220 (Covaris, MA, USA) and used for construction of a library with SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Genomic DNA (1 μg) from each tissue sample was sheared using a Covaris S220 (Covaris, MA, USA) and used for the construction of a library using the SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

Ligation:

Article Title: Intratumor heterogeneity inferred from targeted deep sequencing as a prognostic indicator
Article Snippet: In brief, the cancer panel sequencing data were generated by DNA shearing, library construction, and sequencing on a HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA) according to manufacturer’s protocol. .. Libraries were constructed by end repair, A-tailing, paired-end adaptor ligation, amplification, hybridization, indexing, and enrichment using a SureSelectXT reagent kit, HSQ (Agilent Technologies). .. The sequencing reactions were performed with the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (lllumina).

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: 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).

Article Title: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: Genomic DNA (250 ng) from the tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of the library using customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies), according to the manufacturer’s protocol. .. After enriched exome libraries were multiplexed, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina, USA), as described previously [ ].

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: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
Article Snippet: Genomic DNA (250 ng) from each tissue was sheared with Covaris S220 (Covaris, Woburn, MA, USA) and was used for the construction of a library using probes and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol. .. After the enriched exome libraries were multiplexed, the libraries were sequenced using the HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA).

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: Genomic DNA (1 µg) from each FFPE sample was sheared by Covaris S220 (Covaris, MA, USA) and used for construction of a library with SureSelect XT Human All Exon v5 and the 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 a HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA).

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Genomic DNA (1 μg) from each tissue sample was sheared using a Covaris S220 (Covaris, MA, USA) and used for the construction of a library using the SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. After enriched exome libraries were multiplexed, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina).

Generated:

Article Title: Intratumor heterogeneity inferred from targeted deep sequencing as a prognostic indicator
Article Snippet: In brief, the cancer panel sequencing data were generated by DNA shearing, library construction, and sequencing on a HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA) according to manufacturer’s protocol. .. Libraries were constructed by end repair, A-tailing, paired-end adaptor ligation, amplification, hybridization, indexing, and enrichment using a SureSelectXT reagent kit, HSQ (Agilent Technologies).

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: 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).

Article Title: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: Genomic DNA (250 ng) from the tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of the library using customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies), according to the manufacturer’s protocol. .. After enriched exome libraries were multiplexed, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina, USA), as described previously [ ].

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: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
Article Snippet: Genomic DNA (250 ng) from each tissue was sheared with Covaris S220 (Covaris, Woburn, MA, USA) and was used for the construction of a library using probes and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol. .. After the enriched exome libraries were multiplexed, the libraries were sequenced using the HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA).

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: Genomic DNA (1 µg) from each FFPE sample was sheared by Covaris S220 (Covaris, MA, USA) and used for construction of a library with SureSelect XT Human All Exon v5 and the 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 a HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA).

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Genomic DNA (1 μg) from each tissue sample was sheared using a Covaris S220 (Covaris, MA, USA) and used for the construction of a library using the SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. After enriched exome libraries were multiplexed, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina).

Sequencing:

Article Title: Intratumor heterogeneity inferred from targeted deep sequencing as a prognostic indicator
Article Snippet: Paragraph title: Sequencing by customized cancer panel ... Libraries were constructed by end repair, A-tailing, paired-end adaptor ligation, amplification, hybridization, indexing, and enrichment using a SureSelectXT reagent kit, HSQ (Agilent Technologies).

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: 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: 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: Landscape of Actionable Genetic Alterations Profiled from 1,071 Tumor Samples in Korean Cancer Patients
Article Snippet: Genomic DNA was sheared using a Covaris S220 (Covaris, Woburn, MA). .. Target capture was performed using the Sure-Select XT Reagent Kit, HSQ (Agilent Technologies) and a paired-end sequencing library was constructed with a barcode. .. Sequencing was performed on a HiSeq 2500 with 100-bp reads (Illumina, San Diego, CA).

Article Title: Four distinct immune microenvironment subtypes in gastric adenocarcinoma with special reference to microsatellite instability
Article Snippet: Paragraph title: 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: 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.

Article Title: Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker
Article Snippet: Paragraph title: 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.

Article Title: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: Paragraph title: Customized targeted cancer panel sequencing for ALK fusion genes ... Genomic DNA (250 ng) from the tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of the library using customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies), according to the manufacturer’s protocol.

Article Title: ARID1B alterations identify aggressive tumors in neuroblastoma
Article Snippet: Paragraph title: Deep sequencing using CancerSCAN™ ... Genomics DNA (250 ng) from each tissue was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn MA, USA) and used for the construction of a library with CancerSCAN™ probes and a SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol.

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. .. 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: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
Article Snippet: Paragraph title: Targeted sequencing ... Genomic DNA (250 ng) from each tissue was sheared with Covaris S220 (Covaris, Woburn, MA, USA) and was used for the construction of a library using probes and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol.

Article Title: Role of HER2 mutations in refractory metastatic breast cancers: targeted sequencing results in patients with refractory breast cancer
Article Snippet: Paragraph title: Sequencing using a customized cancer panel (CancerSCAN™) ... Genomic DNA (250 ng) from each tissue was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn MA, USA) and used for the construction of a library using CancerSCAN™ probes and a SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol.

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: Paragraph title: Exome sequencing ... Genomic DNA (1 µg) from each FFPE sample was sheared by Covaris S220 (Covaris, MA, USA) and used for construction of a library with SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol.

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Paragraph title: Whole exome sequencing ... Genomic DNA (1 μg) from each tissue sample was sheared using a Covaris S220 (Covaris, MA, USA) and used for the construction of a library using the SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol.

Article Title: Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences
Article Snippet: Paragraph title: Cancer panel sequencing ... For Illumina HiSeq 2500, we used 250 ng of gDNA after shearing DNA with the Covaris S220 (Covaris, Woburn, MA, USA) and constructed library with customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies) as previously described [ ].

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.

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.

Article Title: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: Genomic DNA extraction was performed using the QIAamp DNA mini kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions. .. Genomic DNA (250 ng) from the tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of the library using customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies), according to the manufacturer’s protocol.

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: 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: 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: 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.

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: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
Article Snippet: Genomic DNA (250 ng) from each tissue was sheared with Covaris S220 (Covaris, Woburn, MA, USA) and was used for the construction of a library using probes and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocol. .. Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: Genomic DNA (1 µg) from each FFPE sample was sheared by Covaris S220 (Covaris, MA, USA) and used for construction of a library with SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Genomic DNA (1 μg) from each tissue sample was sheared using a Covaris S220 (Covaris, MA, USA) and used for the construction of a library using the SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification.

Polymerase Chain Reaction:

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: Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker
Article Snippet: 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. .. Sequencing reads were aligned to the UCSC hg19 reference genome (downloaded from http://genome.ucsc.edu ) using Burrows-Wheeler Aligner (BWA) [ ], version0.6.2 with default settings.

Article Title: Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences
Article Snippet: Next, the multiplexed barcoded libraries were enriched by clonal amplification using emulsion polymerase chain reaction (PCR) on Ion Sphere Particles (Ion PGMTemplate 200 Kit) and loaded on an Ion 316 Chip. .. For Illumina HiSeq 2500, we used 250 ng of gDNA after shearing DNA with the Covaris S220 (Covaris, Woburn, MA, USA) and constructed library with customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies) as previously described [ ].

Blocking 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 ( ).

Chromatin Immunoprecipitation:

Article Title: Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences
Article Snippet: Next, the multiplexed barcoded libraries were enriched by clonal amplification using emulsion polymerase chain reaction (PCR) on Ion Sphere Particles (Ion PGMTemplate 200 Kit) and loaded on an Ion 316 Chip. .. For Illumina HiSeq 2500, we used 250 ng of gDNA after shearing DNA with the Covaris S220 (Covaris, Woburn, MA, USA) and constructed library with customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies) as previously described [ ].

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.

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: Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences
Article Snippet: We performed NGS using either Ion AmpliSeq™ Cancer Hotspot Panel v2 with Ion Torrent Personal Genome Machine (PGM, Life Technologies, Grand Island, NY, USA) or a customized cancer panel, CancerSCAN™ with Illumina HiSeq 2500 (Illumina, USA) as previously described [ , ]. .. For Illumina HiSeq 2500, we used 250 ng of gDNA after shearing DNA with the Covaris S220 (Covaris, Woburn, MA, USA) and constructed library with customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies) as previously described [ ].

Concentration Assay:

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: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: The Nanodrop 8000 UV-Vis spectrometer (Thermo Scientific Inc., DE, USA), Qubit 2.0 Fluorometer (Life Technologies), and 2200 TapeStation Instrument (Agilent Technologies, Santa Clara, CA, USA) were used to check the concentration, purity, and degradation of extracted genomic DNA. .. Genomic DNA (250 ng) from the tissues was sheared by the Covaris S220 (Covaris, Woburn, MA, USA) and used for the construction of the library using customized RNA baits and the SureSelect XT reagent kit, HSQ (Agilent Technologies), according to the manufacturer’s protocol.

High Throughput Screening Assay:

Article Title: Landscape of Actionable Genetic Alterations Profiled from 1,071 Tumor Samples in Korean Cancer Patients
Article Snippet: Target capture was performed using the Sure-Select XT Reagent Kit, HSQ (Agilent Technologies) and a paired-end sequencing library was constructed with a barcode. .. Sequencing was performed on a HiSeq 2500 with 100-bp reads (Illumina, San Diego, CA).

Staining:

Article Title: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: 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.

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    Agilent technologies sureselectxt reagent kit hsq
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    Agilent technologies hsq
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