RNA sequencing data analysis of the yeast Vanrija (Cryptococcus) humicola strain UJ1 grown on L- and D-aspartate

Published: 10 January 2023| Version 1 | DOI: 10.17632/vhsy73dryt.1
Contributor:
Shouji Takahashi

Description

Supplemental File1: Differential expression genes (DEGs) in the yeast V. humicola strain UJ1 grown on D-asparate as the sole carbon source compared with L-aspartate. Supplemental File2: GO enrichment analysis of the upregulated DEGs in the yeast V. humicola strain UJ1 cells grown on D-aspartate as the sole carbon source compared with L-aspartate. Supplemental File3: GO enrichment analysis of the downregulated DEGs in the yeast V. humicola strain UJ1 cells grown on D-aspartate as the sole carbon source compared with L-aspartate. Supplemental File4: KEGG pathway enrichment analysis of the upregulated DEGs in the yeast V. humicola strain UJ1 cells grown on D-aspartate as the sole carbon source in comparison with L-aspartate. Supplemental File5: KEGG pathway enrichment analysis of the downregulated DEGs in the yeast V. humicola strain UJ1 cells grown on D-aspartate as the sole carbon source in comparison with L-aspartate.

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The raw reads were filtered to remove the reads containing adapter contamination and the reads in which uncertain nucleotides constitute more than 10% of either end and low-quality nucleotides (base quality less than 20) constitute more than 50% of the reads. All clean reads were then aligned to the genome sequence of the yeast V. humicola strain UJ1 (DDBJ/EMBL/GenBank accession numbers BFAH01000001 to BFAH01000046; scaffolds 1 to 19 and 21 to 47, respectively) using the TopHat2 package . Transcript abundance was quantified using HTSeq package v0.6.1, and differentially expressed genes (DEGs) between the growth conditions on L- and D-aspartate were identified using the DEGSeq v1.12.0. The Benjamini–Hochberg false discovery rate (FDR) multiple test correction was applied, and genes with a log2 fold change > 1 or < -1 and with FDR adjusted p-value (q-value) <0.005 were considered to be differentially expressed. Gene Ontology (GO) enrichment analysis was performed using GOSeq package release 2.12. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed using KOBAS v3.0.

Institutions

Nagaoka Gijutsu Kagaku Daigaku

Categories

RNA Sequencing

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