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Sureselectxt mouse all exon capture kit

Manufactured by Agilent Technologies
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The SureSelectXT Mouse All Exon capture kit is a lab equipment product by Agilent Technologies designed to capture and enrich the mouse exome for sequencing applications. It provides comprehensive coverage of the mouse protein-coding regions.

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Lab products found in correlation

Hiseq 2000 sequencing instrument, by Illumina (2 mentions) Hiseq 4000, by Illumina (2 mentions) Purelink genomic dna mini kit, by Thermo Fisher Scientific (2 mentions)

Spelling variants of this product

SureSelectXT kit (18 citations) SureSelectXT Mouse All Exon (7 citations) SureSelectXT mouse exon kit (2 citations)

4 protocols using sureselectxt mouse all exon capture kit

1

Mutational Profiling of Vav1-Myo1f Lymphomas

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For the analysis of the mutational profile of mouse Vav1-Myo1f-induced lymphomas Genomic DNA was isolated from CD4+ T-cells from lymphoma-infiltrated spleens. Paired normal DNA was isolated from the non-T cell fraction or tail clips from the same animals. Exome capture and sequencing were performed at GENEWIZ (South Plainfield, NJ) using the Agilent SureSelectXT Mouse All Exon capture kit (Agilent) and paired-end sequencing (2 × 150 bp) in a HiSeq2000 sequencing instrument (Illumina). We obtained between 26.6M and 80.4M paired-end reads per sample, with an average of 53.7M reads. Data pre-processing for variant discovery was performed using the Genome Analysis Toolkit (GATK) version 4.2.0.0 and Picard tools version 2.26.10 following best practices as outlined in GATK documentation. Reads are aligned to GRCm38 using Burrows-Wheeler Aligner’s maximal exact matches (BWA-MEM) algorithm version 0.7.1. We identified candidate somatic variants as those absent in normal and present in tumor using the Mutect2 algorithm.
Cortes J.R., Filip I., Albero R., Patiño-Galindo J.A., Quinn S.A., Lin W.H., Laurent A.P., Shih B.B., Brown J.A., Cooke A.J., Mackey A., Einson J., Zairis S., Rivas-Delgado A., Antonella Laginestra M., Pileri S., Campo E., Bhagat G., Ferrando A.A., Rabadan R, & Palomero T. (2022). Oncogenic Vav1-Myo1f induces therapeutically targetable macrophage-rich tumor microenvironment in peripheral T cell lymphoma. Cell reports, 39(3), 110695.
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2

Whole Exome Sequencing of Mouse Cell Lines

Cited 1 time
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DNA was extracted using the commercially available Purelink Genomic DNA mini kit (Invitrogen) as per the manufacturer’s instructions. The purity and concentration of the DNA of both cell lines were measured using nanodrop. Whole exome sequencing (WES) was performed on an Illumina HiSeq 4000 machine using libraries prepared with a SureSelectXT Mouse All Exon capture kit (Agilent Technologies, Santa Clara, California, USA), to produce 150 paired end reads sufficient for a mean bait coverage of at least 150×. The sequence reads were aligned to the GRCm38.p6 mouse reference assembly using BWA-MEM V.0.7.17,25 (link) and variants were predicted using the Genome Analysis Toolkit best practices protocol (GATK V.3.7). A set of reference variants for mouse was derived from data generated by the Wellcome Sanger Institute Mouse Genomes Project (available at ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/). Somatic mutations (SMs) were defined as variants present only in the 4T1 sample, while single nucleotide polymorphisms (SNPs) were defined as variants present in both the 4T1 and EpH4-Ev samples. The functional effect of the predicted SMs and SNPs was determined by annotating the variants with snpEff V.4.3T26 (link) using the GRCm38.86 and mm10 databases.
Mohsen M.O., Speiser D.E., Michaux J., Pak H., Stevenson B.J., Vogel M., Inchakalody V.P., de Brot S., Dermime S., Coukos G., Bassani-Sternberg M, & Bachmann M.F. (2022). Bedside formulation of a personalized multi-neoantigen vaccine against mammary carcinoma. Journal for Immunotherapy of Cancer, 10(1), e002927.
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3

Mutational Profiling of Vav1-Myo1f Lymphomas

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For the analysis of the mutational profile of mouse Vav1-Myo1f-induced lymphomas Genomic DNA was isolated from CD4+ T-cells from lymphoma-infiltrated spleens. Paired normal DNA was isolated from the non-T cell fraction or tail clips from the same animals. Exome capture and sequencing were performed at GENEWIZ (South Plainfield, NJ) using the Agilent SureSelectXT Mouse All Exon capture kit (Agilent) and paired-end sequencing (2 × 150 bp) in a HiSeq2000 sequencing instrument (Illumina). We obtained between 26.6M and 80.4M paired-end reads per sample, with an average of 53.7M reads. Data pre-processing for variant discovery was performed using the Genome Analysis Toolkit (GATK) version 4.2.0.0 and Picard tools version 2.26.10 following best practices as outlined in GATK documentation. Reads are aligned to GRCm38 using Burrows-Wheeler Aligner’s maximal exact matches (BWA-MEM) algorithm version 0.7.1. We identified candidate somatic variants as those absent in normal and present in tumor using the Mutect2 algorithm.
Cortes J.R., Filip I., Albero R., Patiño-Galindo J.A., Quinn S.A., Lin W.H., Laurent A.P., Shih B.B., Brown J.A., Cooke A.J., Mackey A., Einson J., Zairis S., Rivas-Delgado A., Antonella Laginestra M., Pileri S., Campo E., Bhagat G., Ferrando A.A., Rabadan R, & Palomero T. (2022). Oncogenic Vav1-Myo1f induces therapeutically targetable macrophage-rich tumor microenvironment in peripheral T cell lymphoma. Cell reports, 39(3), 110695.
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4

Whole Exome Sequencing of Murine Cell Lines

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DNA was extracted using the commercially available Purelink Genomic DNA mini kit (Invitrogen) as per the manufacturer's instructions. The purity and concentration of the DNA of both cell lines were measured using nanodrop. Whole exome sequencing (WES) was performed on an Illumina HiSeq 4000 machine using libraries prepared with a SureSelectXT Mouse All Exon capture kit (Agilent Technologies, Santa Clara, CA, USA), to produce 150 paired end reads sufficient for a mean bait coverage of at least 150x. The sequence reads were aligned to the GRCm38.p6 mouse reference assembly using BWA-MEM v0.7.17 (26) , and variants were predicted using the Genome Analysis Toolkit best practices protocol (GATK v3.7). A set of reference variants for mouse was derived from data generated by the Wellcome Sanger Institute Mouse Genomes Project (available at ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/). Somatic mutations (SMs) were defined as variants present only in the 4T1 sample, while single nucleotide polymorphisms (SNPs) were defined as variants present in both the 4T1 and EpH4-Ev samples. The functional effect of the predicted SMs and SNPs was determined by annotating the variants with snpEff v4.3T (27) using the GRCm38.86 and mm10 databases.
Mohsen M.O., Speiser D.E., Michaux J., Pak H., Stevenson B.J., Vogel M., Inchakalody V., Brot S.d., Coukos G., Dermime S., Bassani‐Sternberg M., & Bachmann M.F. (2021). Bedside formulation of a personalized multi-neoantigen vaccine against mammary carcinoma.
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