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Supplemental Material for Fialkowski et al., 2019

posted on 2019-01-16, 15:40 authored by Allison C. Fialkowski, Denise J. Levy, Dawn E. Watkins-Chow, Joseph W. Palmer, Roshan Darji, Hemant K Tiwari, William J. Pavan, Melissa L. Harris

Supplemental File 1: SNP genotyping data of progeny produced from backcrossing (C57BL/6J x DBA/1J)F1-Tg(DctSox10)/0 females to C57BL/6J males. The sheet named ‘Original Sample Genotypes’ includes the original Illumina SNP genotyping results. The sheet named ‘Converted Sample Genotypes’ includes the genotyping data formatted for evaluation by R/QTL.

Supplemental File 2: Whole skin RNAseq data was retrieved from NCBI GEO using the accession # GSE86315. HTSeq counts from the C57BL/6J and DBA/1J control skin samples (2 males and 2 females per strain all treated with a non-toxic lanolin-derived occlusion cream) were normalized and contrasted to obtain differential expression values using DESeq2. The complete differential expression data including gene symbol, base mean (mean of the normalized counts), log2 fold change, log fold SE, p-value (unadjusted p-value) and p adj (adjusted p-value) is provided.

Supplemental File 3: Wildtype C57BL/6J McSC RNAseq data was retrieved from NCBI GEO using the accession # GSE102271. RNAseq reads were aligned to the Ensembl GRCm38.p5 primary DNA assembly using STAR (v2.5.2b) and normalized read counts (median ratio method) determined using DESeq2. Normalized read counts with a value of 0 were omitted from further analysis. The complete McSC expression data including ensemble gene id, normalized read counts across each biological sample, base mean (mean of the normalized counts), gene symbol, and percent rank is provided.

Supplemental File 4: Output from analysis of DNA variants between C57BL/6J and DBA/1J using PROVEAN. Summary and detailed results are provided. Within the detailed results, information on each variant includes the protein ID, length, strand, codon change, pos (position), residue ref (reference), residue alt (alternate), type (of mutation), score (provean), prediction (provean), gene id and gene name.


Article title

Identification of Gene Variants Associated with Melanocyte Stem Cell Differentiation in Mice Predisposed for Hair Graying

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    G3: Genes|Genomes|Genetics



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