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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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