Agilent sureselectxt mouse all exon kit

Manufactured by Agilent Technologies

Sourced in United States

The Agilent SureSelectXT Mouse All Exon kit is a tool used for targeted enrichment of mouse exonic regions. It provides a comprehensive solution for capturing and sequencing the mouse exome.

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Lab products found in correlation

Qubit 2.0 dna hs assay, by Thermo Fisher Scientific (1 mentions) Qubit 2.0 dna hs assay, by Agilent Technologies (1 mentions) Tapestation high sensitivity d1000 assay, by Agilent Technologies (1 mentions) Tapestation genomic dna assay, by Agilent Technologies (1 mentions) Novaseq, by Illumina (1 mentions) Quantstudio 5 system, by Thermo Fisher Scientific (1 mentions) Hydrodynamic shearing system, by Covaris (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions) Agilent bioanalyzer 2100 system, by Agilent Technologies (1 mentions) Ampure xp system, by Beckman Coulter (1 mentions) Ion pi hi q chef kit, by Thermo Fisher Scientific (1 mentions) Dynabeads myone streptavidin t1 beads, by Thermo Fisher Scientific (1 mentions) E gel sizeselect 2 agarose gel, by Thermo Fisher Scientific (1 mentions) Dna high sensitivity kit, by Thermo Fisher Scientific (1 mentions) Ion pi hi q sequencing 200 kit, by Thermo Fisher Scientific (1 mentions) Puregene kit, by Qiagen (1 mentions) Dneasy blood tissue kit, by Qiagen (1 mentions) Agencourt ampure xp bead, by Beckman Coulter (1 mentions)

4 protocols using agilent sureselectxt mouse all exon kit

Exome Sequencing of Mouse Tumors

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Genomic DNA was extracted using QIAamp DNA Mini Kit. Extracted genomic DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher) and the quality of DNA was assessed by Tapestation Genomic DNA Assay (Agilent Technologies). Library construction was performed using Agilent SureSelectXT Mouse All Exon kit (Agilent Technologies) per the manufacturer’s recommendations. Library quantity and quality were assessed with Qubit 2.0 DNA HS Assay, Tapestation High Sensitivity D1000 Assay (Agilent Technologies) and QuantStudio 5 System (ThermoFisher). Multiple libraries were then pooled and sequenced on an Illumina NovaSeq (Illumina) with 2 × 150-bp paired-end mode targeting 80 million reads per sample (~120X coverage). SNPs and small insertions and deletions (InDels) of each sample were called by the Genome Analysis Toolkit (GATK)^{74 (link)} and annotated by ANNOVA^{75 (link)}. Additional filters were then applied to only retain variants that are either nonsynonymous exonic variants or splicing variants of genes included in the Cancer Gene Census Tier 1 list (https://cancer.sanger.ac.uk/cosmic). Germline information of these variants was annotated using the Mouse Genome Informatics database (http://www.informatics.jax.org/).

Wu Z., Zhou J., Zhang X., Zhang Z., Xie Y., Liu J.B., Ho Z.V., Panda A., Qiu X., Cejas P., Cañadas I., Akarca F.G., McFarland J.M., Nagaraja A.K., Goss L.B., Kesten N., Si L., Lim K., Liu Y., Zhang Y., Baek J.Y., Liu Y., Patil D.T., Katz J.P., Hai J., Bao C., Stachler M., Qi J., Ishizuka J.J., Nakagawa H., Rustgi A.K., Wong K.K., Meyerson M., Barbie D.A., Brown M., Long H, & Bass A.J. (2021). Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence. Nature genetics, 53(6), 881-894.

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Exome Sequencing of Mouse Samples

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1 μg genomic DNA per sample was used as input material for the DNA sample preparation. Sequencing libraries were generated using Agilent SureSelectXT Mouse All Exon kit (Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. Sequencing was performed on an Illumina platform, followed by bioinformatics analyses. Exome sample preparation, sequencing, and data analysis were performed by Novogene (Cambridge, UK) according to established pipelines.

Maetzig T., Lieske A., Dörpmund N., Rothe M., Kleppa M.J., Dziadek V., Hassan J.J., Dahlke J., Borchert D, & Schambach A. (2022). Real-Time Characterization of Clonal Fate Decisions in Complex Leukemia Samples by Fluorescent Genetic Barcoding. Cells, 11(24), 4045.

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Whole Exome Sequencing of FVBW-17 Cells

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DNA from FVBW-17 parental and clonal cell lines was extracted using QIAamp DNA Mini Kit (Qiagen). For sample preparation, 1 μg genomic DNA per sample was used as input. Sequencing libraries were prepared using Agilent SureSelectXT Mouse All Exon kit (Agilent Technologies). Briefly, fragmentation was carried out using the hydrodynamic shearing system (Covaris) to generate 180–280 bp fragments, and remaining overhangs were converted into blunt ends. After adenylation of the 3′ ends, adapter oligonucleotides were ligated and selectively enriched in a PCR. The libraries were then hybridized with a biotin-labeled probe, and magnetic beads with streptomycin were used to capture exons. Captured libraries were enriched in a PCR to add index tags to prepare for hybridization. Products were purified using the AMPure XP system (Beckman Coulter) and quantified using the Agilent Bioanalyzer 2100 System.

Stabile L.P., Kumar V., Gaither-Davis A., Huang E.H., Vendetti F.P., Devadassan P., Dacic S., Bao R., Steinman R.A., Burns T.F, & Bakkenist C.J. (2021). Syngeneic tobacco carcinogen–induced mouse lung adenocarcinoma model exhibits PD-L1 expression and high tumor mutational burden. JCI Insight, 6(3), e145307.

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Targeted Exome Sequencing of Tumor Samples

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Genomic DNA from tumors and blood was purified using the QIAGEN Puregene Kit (catalog 158445). DNA from buffy coats was purified using QIAGEN DNeasy Blood & Tissue Kit (catalog 69504). The Genomic DNA was sheared with Ion Shear Plus Reagents (Ion Plus Fragment Library Kit) and size-selected with Agencourt AMPure XP beads (Beckman Coulter). DNA fragments with a base pair peak of 100–150 bp were ligated with Ion adapters, purified with Agencourt AMPure XP beads, and PCR-amplified. Then, 750 ng of the adapter-ligated DNA library was hybridized to SureSelect capture library (Agilent SureSelect XT Mouse All Exon Kit) for 20 hours at 65°C. The hybrid capture library was selected using Dynabeads MyOne Streptavidin T1 beads (Life Technologies). The captured library was amplified and purified with AMPureXP beads, and quality was assessed on the High Sensitivity DNA Kit (Life Technologies) on the Agilent Bioanalyzer. We selected a 220 bp peak using E-Gel SizeSelect 2% agarose gel (Life Technologies). The final library was purified and quality assessed on High Sensitivity DNA Bioanalyzer chip (Life Technologies). Templates were prepared using the Ion PI Hi-Q Chef Kit (Life Technologies) on the Ion Chef platform and sequenced on an Ion Proton Sequencer on a PI v3 chip using Ion PI Hi-Q Sequencing 200 Kit (Life Technologies).

Osei-Hwedieh D.O., Sedlacek A.L., Hernandez L.M., Yamoah A.A., Iyer S.G., Weiss K.R, & Binder R.J. (2023). Immunosurveillance shapes the emergence of neo-epitope landscapes of sarcomas, revealing prime targets for immunotherapy. JCI Insight, 8(13), e170324.

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