28.直腸カルチノイド(第609回千葉医学会例会・第1外科教室談話会)

Basic PELE-seq SNP-calling scripts. The basic commands used for PELE-Seq analysis are provided as a shell script. (TXT 11 kb

Additional file 1: of Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes

The un-activated sperm proteome of C. elegans. The majority of the proteome is comprised of the Nematode-Specific Peptide family, group D (NSPD) and the Major Sperm Protein (MSP). Protein abundance is shown as the relative mean normalized spectrum abundance frequency. Proteins found to be unique to either the membranous organelle or activated sperm proteomes are highlighted in teal, while proteins found in both proteomes are shown in gray. Proteins shown in white were not identified in the membranous organelle or activated sperm proteomes, but were found in the previously published un-activated spermatid proteome of Ma et al. [21]. (PDF 863 kb

Additional file 6: of Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes

Sequence alignments for the Nematode-Specific Peptide family, group F (NSPF) orthologous genes. Amino acid sequence is largely conserved across orthologs. (PDF 158 kb

Additional file 2: of Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes

Proteome data for C. elegans and C. remanei. Un-activated spermatid, membranous organelle, and active sperm proteome data for both species analyzed, including WormBase gene identifiers, protein abundances, and peptide coverage. (XLSX 64 kb

Additional file 9: of Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes

Functional assays of the Nematode-Specific Peptide family, group F (NSPF) gene family. The fecundity data for total reproductive success and competitive reproductive success of NSPF knockout males. (XLSX 60 kb

Additional file 5: of Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes

An unrooted maximum likelihood phylogeny for the Nematode-Specific Peptide family, group D (NSPD). Genes tend to cluster within species and do not recapitulate an evolutionary history of gene orthology. Asterisks denote bootstrap values greater than 80%. (PDF 945 kb

Additional file 7: of Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes

Unrooted maximum likelihood phylogenies for the Nematode-Specific Peptide family, group F (NSPF) orthologous genes. Overall, gene trees recapitulate species relationships. Asterisks denote bootstrap values greater than 80%. (PDF 867 kb

Additional file 4: of Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes

Consensus sequence alignments for the Nematode-Specific Peptide family, group D (NSPD). The amino acid sequence is largely conserved, except for the species-specific amino acid repeats in the middle of the gene. (PDF 79 kb

Additional file 5: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

PCR errors that result in false positive SNPs when using unfiltered ORP data. Overlapping paired-end read libraries sequenced to 10,000× OPE depth contained 109 false positive SNPs when rare variants were called with Lofreq, using default parameters with no minimum allele frequency cutoff. These putative PCR errors are predominately C > T transitions are are found in distinct clusters throughout the genome. This data is also included as a spreadsheet in Additional file 3. (PDF 18 kb

Palopoli_elegans_spermcompetition

Sperm competition results for C. elegans lines evolved in the presence of high and low male-male competitio