Gene tagging and gene deletion resources for Leishmania mexicana MNYC/BZ/62/M379 Cas9/T7 strain
DOI10.5281/zenodo.14621467Zenodo14621467MaRDI QIDQ6709253FDOQ6709253
Dataset published at Zenodo repository.
Richard John Wheeler, Jeremy Charles Mottram, Carolina Moura Costa Catta-Preta, U. Dobramysl, Tom Beneke, Eva Gluenz
Publication date: 9 January 2025
Copyright license: Creative Commons Attribution 4.0 International
primers_barcodes.csv: List of primer sequences necessary for N and C terminus gene tagging, as well as gene deletion in the Leishmania mexicana MNYC/BZ/62/M379 Cas9/T7 strain. Each row contains the gene name and the DF (downstream forward), DR (downstream reverse), DSG (downstream guide sRNA), UF (upstream forward), UFB (upstream forward including a gene-unique 17nt barcode sequence), UR (upstream reverse), USG (upstream guide sRNA), VF (verification forward) and VR (verification reverse) primer sequences. Empty cells indicate that it was not possible to design this primer for this gene. Guide sRNA perfect match and off-target counts are included as well. The primer sequences were designed using LeishGEdit (http://www.leishgedit.net). Barcode sequences and assigned IDs for the unique identification of knock-out or tagged strains are included as separate columns. For recommended methods for endogenous tagging or gene deletion see Beneke et al., R. Soc. Open Sci.4170095 (2017), for generating barcoded deletion mutants see Beneke and Gluenz, Mol. Biochem. Parasitol. 239 (2020). genome.gff: Annotated genome of the L. mexicana MNYC/BZ/62/M379 strain, genetically modified to express T7 RNA polymerase and Cas9. The annotation is provided in a combined GFF3 / FASTA format that also includes the sequences of the chromosomes and small contigs. The annotation also specifies polyadenylation sites (PAS features) and splice leader acceptor sites (SLAS features) which were used to refine the boundaries of protein-coding sequences as well as 3' and 5' untranslated regions over the reference genome of L. mexicana MNYC/BZ/62/M379. c9t7_sequences.fasta: Raw chromosome and contig sequences in FASTA format. c9t7_transcripts.fasta: mRNA transcript sequences in FASTA format (includes 5' and 3' UTRs). c9t7_transcript_CDSs.fasta: Coding sequences in FASTA format. c9t7_predicted_protein_sequences.fasta: Predicted protein amino acid sequences in FASTA format. Note: This version provides an update for c9t7_transcript_CDSs.fasta, c9t7_predicted_protein_sequences.fasta andgenome.gff,correcting an off-by-one sequence coordinate in 48 of the the protein-coding genes.
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