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ABSTRACT: Pichia kluyveri X31-10

PROVIDER: PRJNA723478 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14292670.fastq.gz	Fastqsanger.gz
	SRR14292671.fastq.gz	Fastqsanger.gz
	SRR14292672.fastq.gz	Fastqsanger.gz
	SRR14292673.fastq.gz	Fastqsanger.gz
	SRR14292674.fastq.gz	Fastqsanger.gz

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Pichia kluyveri strain:X31-10

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Transcription profiling by array of Saccharomyces cerevisiae strain VL3 with or without the the co-inoculation of a second yeast species, Pichia kluyveri (PKKR1).

Project description:Replicate cultres of Saccharomyces cerevisiae strain VL3 (a commercial wine strain) were inititaed with and without the the co-inoculation of a second yeast species, Pichia kluyveri (PKKR1). In addition replicate cultures of Pichia kluyveri were initiated. The media for all cultures was sterile Sauvignon blanc grape juice. Triplicates of each treatment were destructively harvested at days 2, 9 and 16 of fermentation and RNA extracted. RNA from S. cerevisiae could not be preferentially extracted from co-ferments. P. kluyveri genome has not been sequenced and so homology to S. cerevisiae probes on the array could not be accurately estimated. We extracted RNA from the P. kluyveri single ferments and hybridised them to the S. cerevisiae arrays to control for this. These species diverged over 100 MYA, and we did not observe abundant homology by way of cross hybridisation. The mean probe intensity for P. kluyveri cDNA was 17-fold lower than for S. cerevisiae, but some probes reported reasonable signal. The intensity distribution of these probes fit a log-normal distribution (P<0.01). 97% of the distribution fell below one-thirtieth of the S. cerevisiae maximum intensity: the remaining 3%, comprising 429 probes, potentially have reasonable homology to P. kluyveri cDNA and we removed these from all analyses. Please see associated additional file 'removePKKR1.r' R code to achieve this.

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Project description:Pichia kluyveri isolate:APC 11.10 B Genome sequencing

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RNA-Seq of lung tissue from WT or interleukin-1alpha nuclear localisation sequence mutant mice infected with influenza A

Project description:We generated a mouse with a mutated IL-1alpha nuclear localisation sequence, causing loss of pro-IL-1alpha nuclear localisation. We tested whether this loss of nuclear pro-IL-1alpha affected the response of these mice to Influenza A infection. WT or mNLS mice were anaesthetized by 2.5% inhalation isoflurane and intranasally infected with 10^3 PFU of the IAV strain X31 (H3N2), in a volume of 30 µL PBS, on day 0. Infected WT and mNLS mice, and heterozygous control uninfected mice, were culled on day 7 post-IAV X31 infection, and the lung RNA was extracted.

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RNA-Seq of Influenza A virus infected THP-1 cells at different timepoint

Project description:THP-1 cells were infected by IAV virus strain X31 with a MOI=10, and cells were collected at 3 timepoints:0 hr, 24 hr and 48 hr post-infection. Each timepoint has 3 biological replicates.

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Sef1-dependent gene expression in Lachancea kluyveri

Project description:To understand the Sef1-dependent gene expression in Lachancea kluyveri under both fermentative and respiratory conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of Lachancea kluyveri wild type and sef1 deletion mutant under both YPD and YPGly conditions.

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Project description:To understand the highly active Sef1-VP16 dependent gene expression in Lachancea kluyveri under both fermentative and respiratory conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of Lachancea kluyveri wild type and SEF1-VP16 gain-of-function mutant under both YPD and YPGly conditions.

2019-04-26 | GSE130300 | GEO

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