All the DNA amplicons from RT-qPCR were sequenced and analyzed in an ABI Prism ® 310 Genetic Analyser (Applied Biosystems, Foster City) using standard sequencing protocols described in Falavigna et al. (2014) (link). Sequence analysis was carried out with DNA Sequencing Analysis Software v5 (Applied Biosystems, Foster City) and MEGA7 software (http://www.megasoftware.net/home). Sequences were compared to the grapevine reference ('Pinot Noir' PN40024) genome 12Xv1.
Dna sequencing analysis software v5
Manufactured by Thermo Fisher Scientific
Sourced in United States
DNA Sequencing Analysis Software v5.2 is a software application designed to analyze DNA sequencing data. It provides core functionalities for processing, visualizing, and interpreting sequencing results.
Automatically generated - may contain errors
Lab products found in correlation
Abi prism 310 genetic analyser, by Thermo Fisher Scientific (3 mentions)
Bigdye terminator cycle sequencing kit, by Thermo Fisher Scientific (2 mentions)
Mutation surveyor software, by SoftGenetics (2 mentions)
Seqscape software v2, by Thermo Fisher Scientific (1 mentions)
Bigdye terminator cycle sequencing kit v3, by Thermo Fisher Scientific (1 mentions)
3500 genetic analyzer, by Thermo Fisher Scientific (1 mentions)
3500 series genetic analyzer, by Thermo Fisher Scientific (1 mentions)
Qiaamp dna blood mini kit, by Qiagen (1 mentions)
11 protocols using dna sequencing analysis software v5
1
Grapevine Genome Sequence Analysis
2
Grapevine Genome Sequence Analysis
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All the DNA amplicons from RT-qPCR were sequenced and analyzed in an ABI Prism ® 310 Genetic Analyser (Applied Biosystems, Foster City) using standard sequencing protocols described in Falavigna et al. (2014) (link). Sequence analysis was carried out with DNA Sequencing Analysis Software v5 (Applied Biosystems, Foster City) and MEGA7 software (http://www.megasoftware.net/home). Sequences were compared to the grapevine reference ('Pinot Noir' PN40024) genome 12Xv1.
3
Grapevine Genome Sequence Analysis
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All the DNA amplicons from RT-qPCR were sequenced and analyzed in an ABI Prism ® 310 Genetic Analyser (Applied Biosystems, Foster City) using standard sequencing protocols described in Falavigna et al. (2014) (link). Sequence analysis was carried out with DNA Sequencing Analysis Software v5 (Applied Biosystems, Foster City) and MEGA7 software (http://www.megasoftware.net/home). Sequences were compared to the grapevine reference ('Pinot Noir' PN40024) genome 12Xv1.
4
Genomic Profiling of Canine Melanoma
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Genomic DNA sequencing was performed on six genes that frequently harbour recurrent somatic mutations in human melanoma subtypes: Braf, Nras, Gna11, Gnaq, Mitf and p53 (Additional file 2 ). The genes were sequenced in the canine tissue-derived genomic DNA isolated from the Dog_1 primitive tumor, the Dog_1 engrafted tumor and Ocr_OCMM1X cells, as well from the Dog_2 primitive tumor, and the Dog_2 engrafted tumor, and the primary derived and Ocr_OCMM2X cells. Each gene was sequenced from the genomic DNA, with the Sanger method, as previously described [17 (link)]. Data were analyzed with DNA Sequencing Analysis software v5.2 (Applied Biosystems). The presence of somatic mutations was assessed by comparing DNA sequences from the sample to the CanFam3 reference dog sequence using Seqscape software v2.5 (Applied Biosystems™, Foster City, CA, USA).
5
TB Resistant Strain Sequencing
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Sequencing of the RDR of the rpoB (codon 507-533), katG (codon 315) and promoter region of inhA was performed for the isolates with discordant results for rifampicin and isoniazid according to conventional DST and between both molecular methods (GenoType MTBDRplus and TB-SPRINT), as described previously (de Oliveira et al. 2003 (link)) using an ABI Prism 3100xl DNA sequencer (Applied Biosystems). Nucleotide sequences were analysed by the Applied Biosystems DNA Sequencing Analysis Software v5.2.
6
Bioinformatics Pipeline for Sequence Analysis
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Raw sequence trace files were performed by DNA Sequencing Analysis Software v5.2 (Applied Biosystems) to obtain base-calling with quality scores. The low quality sequences (quality score <55) and the short sequences (< 100 bp) were given up. The vector and adaptor sequences were detected by DNAMAN 7.0 software and removed. All unique genes were searched against the NCBI database with the basic local alignment search tool (BLASTX and BLASTN) (http://blast.ncbi.nlm.nih.gov ). The functional categories of all unique genes were performed according to Gene Ontology [14 (link)].
7
Fluorescent Protein Sequencing Protocol
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DNA sequencing was performed using the ABI BigDye Terminator Cycle Sequencing Kit v1.1 or v3.1 according to the manufacturer's instructions on a Gene Amp 9700 PCR machine. The sequence fragments were detected on an ABI 3130XL Genetic Analyzer. Samples were then analyzed and base-called using the Applied Biosystems DNA Sequencing Analysis Software V5.2. The following primers were used to confirm the structures of the break points: 5’BP:f_Nodal_10317: CGC CCT CTT CTG GAG TGT CTG A; 3’BP:r_Nodal_11870: GCA TCA CTC AGG TCG CTG GGT CAA ACA CA. For recombinants generated by single-stranded oligonucleotide-directed recombineering, the primers used for detecting recombinants were also used to confirm the expected breakpoint structure (see Oligonucteotides section below). Primers for the fluorescent protein coding sequences: f_Str_588: CGC CTA CAT CGT CGG CAT CAA GTT; r_Str_145: CGG TCT GGG TGC CCT CGT A; f_YFP/Str_1: ATG GTG AGC AAG GGC GAG GA; and f_YFP_411: CCT GGG GCA CAA GCT GGA GTA CAA CTA. There was no need to use additional primers for sequencing recombinants generated by single-stranded oligonucleotide-directed recombineering because the modifications encompassed short DNA sequences.
8
Fluorescent Protein Sequencing Protocol
9
Alliinase Sequence Analysis and Comparison
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Sequencing reactions were performed using a BigDye Terminator Cycle Sequencing Kit v.3.1, according to the Applied Biosystems protocol (Foster City, USA). The data were analyzed using Applied Biosystems DNA Sequencing Analysis Software V5. 2.
The sequences were subsequently analyzed using BLAST tools [39 (link)] and compared with CLUSTAL-W softwarehttp://www.ebi.ac.uk/Tools/msa/clustalw2/ [40 (link)] and MEGA version 5.2 http://www.megasoftware.net/ [41 (link)].
Plant alliinase nucleotide sequences with high similarity (E-value <0.02) to those obtained from cv. Jovan were retrieved from GenBankhttp://www.ncbi.nlm.nih.gov/ based on the BLASTn results [39 (link)]. The exons and introns of the genomic sequences were identified by comparing our sequences with A.sativum mRNA encoding the precursor alliinase sequence [GenBank: Z12622.1] using SPLIGN software http://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi [42 (link)] and MEGA software version 5.2 http://www.megasoftware.net/ [41 (link)].
The sequences were subsequently analyzed using BLAST tools [39 (link)] and compared with CLUSTAL-W software
Plant alliinase nucleotide sequences with high similarity (E-value <0.02) to those obtained from cv. Jovan were retrieved from GenBank
10
Confirmation of ASIC5 Variant by Sanger Sequencing
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Whole-genome result was confirmed using Sanger sequencing. The presence of the homozygous NM_017419.3:c.680G>T in the proband and heterozygous in the parents were confirmed using Sanger sequencing. Highly specific primers (ASIC5F: 5′-CAGATAAAAACATGTTTCCATACATCTTCAG-3′ and ASIC5R: 5′- TTGTGGCATGAACATTCCCTGGA-3′) were designed, and the selected region of the gene was amplified [PCR recipe: MOLEQULE-ON absolute master mix 12.5 μl, ASIC5F 1 μl (10 nM), ASIC5R 1 μl (10 nM), DNA Template 25 ng, and Dis H2O to 25 μl; temperature profile: 95°C for 10 min; 35 cycles of 95°C/60 s, 60°C/60 s, 72°C/60 s; and 72°C for 5 min] and sequenced using BigDye Terminator Cycle Sequencing Kit (Thermo Fisher Scientific, Inc., Waltham, MA, USA). Amplified PCR product (691 bp) of the ASIC5 gene region was purified and sequenced using Genetic Analyzer 3500 (Thermo Fisher Scientific, Inc.) at the Department of Genetic Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University (Dammam, Saudi Arabia). Sequences were analyzed using mutation surveyor software (Softgenetics, US) and DNA sequencing analysis software v.5.3 (Applied Biosystem; Thermo Fisher Scientific, Inc.).
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