Dna sequencing analysis software version 5

Manufactured by Thermo Fisher Scientific

Sourced in United States

DNA Sequencing Analysis software, version 5.2, is a bioinformatics application designed for the analysis of DNA sequencing data. The software provides tools for processing, visualizing, and interpreting nucleotide sequence information.

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Lab products found in correlation

Applied biosystems 3130xl genetic analyzer, by Thermo Fisher Scientific (4 mentions) Sequencher version 4, by Gene Codes (4 mentions) Rneasy kit, by Qiagen (2 mentions) Qiaquick pcr purification kit, by Qiagen (2 mentions) Abi prism bigdye terminator cycle ready reaction kit v3, by Thermo Fisher Scientific (2 mentions) Omniscript reverse transcriptase, by Qiagen (2 mentions) Abi prism bigdye terminator kit v3, by Thermo Fisher Scientific (2 mentions) Exonuclease 1, by Thermo Fisher Scientific (1 mentions) Shrimp alkaline phosphatase, by Promega (1 mentions) Taq polymerase, by Avantor (1 mentions) Gentra puregene purification kit, by Qiagen (1 mentions) Sequencher version 5, by Gene Codes (1 mentions) Abi prism bigdye terminator v1.1 cycle sequencing kit, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

DNA sequencing (32 citations) Sequencing Analysis 5.2 (27 citations) Sequencing Analysis software (27 citations) Sequencing Analysis Software Version 5.2 (22 citations) DNA Sequencing Analysis Software (5 citations) Sequencing Analysis Software 5.1 (4 citations)

5 protocols using dna sequencing analysis software version 5

DOCK8 Gene Sequencing from Blood Samples

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Genomic DNA and RNA of controls and patients were isolated from either whole blood or peripheral blood mononuclear cells (PBMCs). RNA was isolated using RNeasy Kit (Qiagen) according to manufacturer’s instructions. RNA was reverse transcribed using Omniscript reverse transcriptase (Qiagen). Coding genomic sequences and cDNA of DOCK8 were amplified and purified using the QIAquick PCR purification kit (Qiagen). Primer sequences are available upon request. Purified PCR products were sequenced with the ABI PRISM BigDye Terminator cycle ready reaction kit V3.1 (Applied Biosystems, Foster City, CA) using the PCR primers as sequencing primers. The sequencing was performed on a 3130xl Applied Biosystems Genetic Analyzer, and the data were analyzed with DNA Sequencing Analysis software version 5.2 (Applied Biosystems) and Sequencher™ version 4.8 (Gene Codes Corporation, Ann Arbor, USA).

Engelhardt K.R., Gertz E.M., Keles S., Schäffer A.A., Sigmund E.C., Glocker C., Saghafi S., Pourpak Z., Ceja R., Sassi A., Graham L.E., Massaad M.J., Mellouli F., Ben-Mustapha I., Khemiri M., Kilic S.S., Etzioni A., Freeman A.F., Thiel J., Schulze I., Al-Herz W., Metin A., Sanal Ö., Tezcan I., Yeganeh M., Niehues T., Dueckers G., Weinspach S., Patiroglu T., Unal E., Dasouki M., Yilmaz M., Genel F., Aytekin C., Kutukculer N., Somer A., Kilic M., Reisli I., Camcioglu Y., Gennery A.R., Cant A.J., Jones A., Gaspar H.B., Arkwright P.D., Pietrogrande M.C., Baz Z., Al-Tamemi S., Lougaris V., Lefranc G., Megarbane A., Boutros J., Galal N., Bejaoui M., Barbouche M.R., Geha R.S., Chatila T.A, & Grimbacher B. (2015). The extended clinical phenotype of 64 patients with DOCK8 deficiency. The Journal of allergy and clinical immunology, 136(2), 402-412.

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Sequencing of STAT3 Coding Sequences

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Genomic DNA and RNA was isolated using RNeasy Kit (Qiagen) according to manufacturer's instructions. RNA was reverse transcribed using Omniscript reverse transcriptase (Qiagen). Coding genomic sequences and cDNA of STAT3 were amplified and purified using the QIAquick PCR purification kit (Qiagen). Primer sequences are available upon request. Purified PCR products were sequenced with the ABI PRISM BigDye Terminator cycle ready reaction kit V3.1 (Applied Biosystems, Foster City, CA, USA) using the PCR primers as sequencing primers. The sequencing was performed on a 3130xl Applied Biosystems Genetic Analyzer, and the data were analysed with DNA Sequencing Analysis software, version 5.2 (Applied Biosystems) and Sequencher™ version 4.8 (Gene Codes Corporation, Ann Arbor, MI, USA).

Tang D., Zhao D., Wu Y., Yao R., Zhou L., Lu L., Gao W, & Sun Y. (2018). The miR‐3127‐5p/p‐STAT3 axis up‐regulates PD‐L1 inducing chemoresistance in non‐small‐cell lung cancer. Journal of Cellular and Molecular Medicine, 22(8), 3847-3856.

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STAT1 Mutation Screening Protocol

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Genomic DNA of patients and family members was isolated from whole blood (Gentra Puregene purification kit, Qiagen, Crawley, United Kingdom). To assess the presence of STAT1 mutations, all coding exons of STAT1 were amplified by PCR according to standard protocols with Taq polymerase (PeqLab, Fareham, United Kingdom). PCR products were purified using shrimp alkaline phosphatase (Promega, Madison, Mich) and Exonuclease I (Thermo Scientific, Waltham, Mass). Primer sequences and PCR amplification conditions are available on request. The amplified DNA fragments were subsequently sequenced with the ABI PRISM BigDye Terminator kit v3.1 (Applied Biosystems, Foster City, Calif). Sequencing was performed using the 3130xl Applied Biosystems Genetic Analyzer, DNA Sequencing Analysis software, version 5.2 (Applied Biosystems), and Sequencher, version 4.8 (Gene Codes Corp, Ann Arbor, Mich).

Depner M., Fuchs S., Raabe J., Frede N., Glocker C., Doffinger R., Gkrania-Klotsas E., Kumararatne D., Atkinson T.P., Schroeder HW J.r., Niehues T., Dückers G., Stray-Pedersen A., Baumann U., Schmidt R., Franco J.L., Orrego J., Ben-Shoshan M., McCusker C., Jacob C.M., Carneiro-Sampaio M., Devlin L.A., Edgar J.D., Henderson P., Russell R.K., Skytte A.B., Seneviratne S.L., Wanders J., Stauss H., Meyts I., Moens L., Jesenak M., Kobbe R., Borte S., Borte M., Wright D.A., Hagin D., Torgerson T.R, & Grimbacher B. (2015). The Extended Clinical Phenotype of 26 Patients with Chronic Mucocutaneous Candidiasis due to Gain-of-Function Mutations in STAT1. Journal of Clinical Immunology, 36, 73-84.

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Sequencing of DOCK8 Exons

Cited 1 time

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Genomic DNA and total RNA were prepared from blood, and cDNA was synthesized as previously described [1 (link)]. Exons and flanking intron/exon boundaries from DOCK8 were amplified from genomic DNA by PCR according to standard protocols with Taq polymerase. PCR products were purified and the DNA was sequenced with the ABI PRISM BigDye Terminator kit V3.1 (Applied Biosystems, Foster City, Calif), the 3130xl Applied Biosystems Genetic Analyzer, DNA Sequencing Analysis software, version 5.2 (Applied Biosystems), and Sequencher, version 5.0 (Gene Codes Corp, Ann Arbor, Mich).

Al-Zahrani D., Raddadi A., Massaad M., Keles S., Jabara H.H., Chatila T.A, & Geha R. (2014). Successful Interferon–alpha 2b Therapy for Unremitting Warts in a Patient with DOCK8 Deficiency. Clinical immunology (Orlando, Fla.), 153(1), 104-108.

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Targeted DNA/RNA Sequencing Protocol

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Selected target fragments (prioritized based on phenotypic information and NGS data) were amplified from genomic DNA and cDNA, when available, using a standard PCR protocol. Primer sequences are available upon request. Amplicons were examined by applying 2.5 µl of each PCR reaction on a 1.3% agarose gel. PCR products were purified using ExoSAP-IT (USB, Cleveland, Ohio, USA) according to the protocol and then sequenced with the ABI PRISM BigDye Terminator v1.1 cycle sequencing kit (Applied Biosystems, Foster City, CA, USA) using the PCR primers as sequencing primers. The sequencing was performed on an ABI 3730 or ABI 3130xl Prism DNA Analyzers, and data analyzed with DNA Sequencing Analysis software, version 5.2 (Applied Biosystems) and Sequencher version 4.7 (Gene Codes Corporation, Ann Arbor, USA).

Moens L.N., Falk-Sörqvist E., Asplund A.C., Bernatowska E., Smith C.I, & Nilsson M. (2014). Diagnostics of Primary Immunodeficiency Diseases: A Sequencing Capture Approach. PLoS ONE, 9(12), e114901.

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