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Additional file 3 of Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus)
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Carrier, Alexandra; Prunier, Julien; Poisson, William; Trottier-Lavoie, Mallorie; Gilbert, Isabelle; Cavedon, Maria; Pokharel, Kisun; Kantanen, Juha; Musiani, Marco; Côté, Steeve D.; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Robert, Claude — 2022 Additional file 3: List of IDs of faulty probes that may yet be found in the resulting vcf https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 1 of Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus)
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Carrier, Alexandra; Prunier, Julien; Poisson, William; Trottier-Lavoie, Mallorie; Gilbert, Isabelle; Cavedon, Maria; Pokharel, Kisun; Kantanen, Juha; Musiani, Marco; Côté, Steeve D.; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Robert, Claude — 2022 Additional file 1: Details for each step of the stacks workflow https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 2 of Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus)
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Carrier, Alexandra; Prunier, Julien; Poisson, William; Trottier-Lavoie, Mallorie; Gilbert, Isabelle; Cavedon, Maria; Pokharel, Kisun; Kantanen, Juha; Musiani, Marco; Côté, Steeve D.; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Robert, Claude — 2022 Additional file 2: List of SNPs positioned on the X chromosome https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 1 of Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights
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Poisson, William; Prunier, Julien; Carrier, Alexandra; Gilbert, Isabelle; Mastromonaco, Gabriela; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Côté, Steeve D.; Robert, Claude — 2023 Additional file 1. Information on 79-mers used for chromosome-level assembly. These Excel files list each oligo with its unique ID and associated probe on a scaffold. The 39-mers genome homologous sequences obtained from running OligoMiner and IFPD scripts are also given with their start and end positions on the scaffold sequence. R_id and F_id are based on 20-mers ID attribution (Additional file 2). The reverse and forward specific 20-mers sequences were assigned according to scaffold number and colour pattern respectively. Each 20-mers forward sequence bears a unique fluorophore (Fluorophore column). Assembled 79-mers oligo sequences were purchased from Genscript. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 2 of Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights
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Poisson, William; Prunier, Julien; Carrier, Alexandra; Gilbert, Isabelle; Mastromonaco, Gabriela; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Côté, Steeve D.; Robert, Claude — 2023 Additional file 2. Orthogonal 20-mers sequences and attribution. Excel file listing the 29 orthogonal 20-mers sequences by ID and used as a reverse or forward primer or a detection oligo. Reverse sequences were used on up to four scaffolds but were unique to a single scaffold in each library. Forward sequences and adapters were used for all libraries. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 3 of Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights
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Poisson, William; Prunier, Julien; Carrier, Alexandra; Gilbert, Isabelle; Mastromonaco, Gabriela; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Côté, Steeve D.; Robert, Claude — 2023 Additional file 3. Primers and detection oligo. Excel file listing the primers used for amplification and transcription reactions and as detection oligo. Reverse primers consist of the 20-mers complementary sequence linked to the 3’ end of the T7 sequence 5’-CGATTGAGGCCGGTAATACGACTCACTATAGGG-3’ [45]. Forward primer 20-mers are linked to the 3’ end of the adapter sequence. The resulting 53-mers reverse primer and 40-mers forward primer oligo were used for PCR. Forward primers were used also for RT-PCR. The fluorophore-linked homolog of the specific 20-mers adapter was the detector of probe binding. These 30 oligo were purchased from IDT as custom standard or HPLC-purified DNA. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 4 of Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights
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Poisson, William; Prunier, Julien; Carrier, Alexandra; Gilbert, Isabelle; Mastromonaco, Gabriela; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Côté, Steeve D.; Robert, Claude — 2023 Additional file 4. Scaffold probe fluorophore associations. Excel file listing the fluorophores used for each scaffold, based on scaffold colour scheme. To create additional colours, some probes were paired with two fluorophores to obtain a mixture. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 1 of Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding
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Poisson, William; Bastien, Alexandre; Gilbert, Isabelle; Carrier, Alexandra; Prunier, Julien; Robert, Claude — 2023 Additional file 1: Table S1. Oligonucleotide information. This Excel file contains four spreadsheets containing oligonucleotide libraries 1 to 4 and one giving the conversion between colour ID and the attributed fluorophore. Each library contains a description of the chromosome, probe and colour attributions for each oligo used in this study. The genome-homologous 39mer are also listed with their respective genomic positions. The “Seq_fin” column contains the final 79mer oligo sequences ordered from Genscript. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 2 of Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding
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Poisson, William; Bastien, Alexandre; Gilbert, Isabelle; Carrier, Alexandra; Prunier, Julien; Robert, Claude — 2023 Additional file 2: Table S2. Primers and detection oligo sequences. This Excel file contains each primer sequence linked to the 3’ end of their attributed specific fluorophore “handle”, the chromosome-specific reverse primers containing the T7 sequence at the 5’ end, and each detection oligo sequence with its attributed fluorophore at the 3’ end. All sequences were purchased from IDT DNA as standard purified oligos except for the detection oligos, which were purchased as HPLC-purified oligos. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 6 of Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding
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Poisson, William; Bastien, Alexandre; Gilbert, Isabelle; Carrier, Alexandra; Prunier, Julien; Robert, Claude — 2023 Additional file 6: Table S3. Correspondence between oligo-banding probes and G-bands and their positions on pig chromosomes. Oligo-banding probe positions are specified starting at the first nucleotide of the first oligonucleotide and ending at the last nucleotide of the last oligonucleotide. G-band positions were estimated by Donaldson et al. [1]. The centromere position relative to oligo-banding probes was confirmed on each chromosome pair. Discrepancy with Donaldson et al. [1] was observed on SSC6, SSC7 and Y. However, our centromere positions match those of Warr et al. [44]. When available, the regions closest to our positioning were included in the Predicted centromere region (start–end)** columns based on Warr et al. [44] results. A discrepancy was observed also for the SSC17 centromere position as Warr et al. [44] have detected it at the SSC17 end compared to our results. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 7 of Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding
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Poisson, William; Bastien, Alexandre; Gilbert, Isabelle; Carrier, Alexandra; Prunier, Julien; Robert, Claude — 2023 Additional file 7: Table S4. Estimated cost of the oligo-banding method. Economic estimation of the main steps associated with the oligo-banding method which are Oligo pool cost, PCR step, in vitro transcription (IVT) step, reverse transcription (RT) step and hybridization total cost including all steps (Total). Costs are expressed in Canadian dollars (CAD) and for the hybridization of one sample (slide). Consumable material costs for each step are included but salaries and laboratory and microscopy basics are not included as they may change between laboratories. https://creativecommons.org/licenses/by/4.0/legalcode

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(Author: Carrier, Alexandra)

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