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Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glycerol

ABSTRACT: Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glycerol

PROVIDER: PRJNA1086178 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28284726_1.fastq.gz	Fastqsanger.gz
	SRR28284726_2.fastq.gz	Fastqsanger.gz

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Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glycerol

Project description:A strand-specific RNA-seq library was constructed for a single sample, specifically the wild-type strain NBRC0988 grown in Yeast Extract Peptone (YP) medium supplemented with 2% w/v glycerol. To prepare the RNA sample, NBRC0988 cells grown overnight were inoculated into 100 mL of liquid Yeast Extract Peptone Dextrose (YPD) medium, with an initial inoculation OD600 of 0.1. These cells were then cultured for 15 hours at 30°C and 250 rpm. Subsequently, the cells were collected by centrifugation at 6,000g for 5 minutes. After being washed twice with phosphate buffer saline (PBS), they were inoculated into fresh 100 mL of YP medium containing 2% w/v glycerol. Following flask culturing at 30°C and 250 rpm for an additional 5 hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction. Total RNA from the sample was isolated using the TRIzol reagent (Invitrogen, Grand Island, USA) and then utilized for high-throughput RNA sequencing. Commercially, the 150-nt paired-end strand-specific RNA-seq libraries (SS_lib_type RF) were generated by Novogene Biotechnology Co. Ltd (Tianjin, China) using the Illumina's Novaseq 6000 platform (Illumina, San Diego, USA).

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Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glucose and xylose

Project description:Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glucose and xylose

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Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glucose and xylose

Project description:Strand-specific RNA-seq libraries were constructed for two samples, including (I) wild-type strain NBRC0988 grown in YEP medium containing 2% w/v glucose;(II) wild-type strain NBRC0988 grown in YEP medium containing 2% w/v xylose. For preparation of RNA samples, NBRC0988 cells grown overnight were inoculated into 100 ml liquid Yeast Extract Peptone Dextrose (YEPD) medium with the initial inoculation amount of OD600= 0.1, and cultured for 15 hours at 30℃ and 250 rpm. The cells were collected by centrifugation at 6,000g for 5 minutes. After washing twice with phosphate buffer saline (PBS), they were inoculated into new 100 mL YEP medium containing 2% w/v glucose or xylose.After flask culturing at 30°C and 250 rpm for an additional 5 hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction. Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The 150-nt paired-end strand-specific RNA-seq libraries (SS_lib_type RF) were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s novaseq 6000 platform (Illumina, San Diego, USA).

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Project description:Cyberlindnera jadinii yeast is a potential sustainable novel feed ingredient for aquaculture industries. Yeasts contain bio-active components and proteins such as beta-glucans, mannans, nucleic acids and proteins that can enhance fish immunity against the disease. In our study, we focused on the characterization of intestinal immunoregulatory pathways in zebrafish (Danio rerio) by quantifying the intestine proteins with isobaric tags for relative and absolute quantitation (iTRAQ) and 2D LC-MS/MS approach. Zebrafish were fed either a control diet (C) or a diet supplemented with autolyzed C. jadinii (ACJ). The KEGG pathways analysis revealed that compared with the control diet, the ACJ yeast diet induced an increased abundance of proteins related to arginine and proline metabolism, phagosome, C-lectin receptor signalling pathway, ribosome pathway and PPAR signalling pathway, which can modulate and enhance the innate response of zebrafish. Moreover, fish fed ACJ yeast diet also showed decreased abundance of proteins associated with inflammatory pathways including apoptosis, necroptosis and ferroptosis pathways. These findings support a mobilization of the innate immune response and a control of inflammatory-related pathways in the intestine of zebrafish. Our findings in the well annotated proteome of zebrafish enabled a detailed investigation of intestinal responses and provide insight into the health-beneficial effects of the yeast species C. jadinii relevant for aquaculture species.

2024-05-24 | PXD040431 | Pride