2025-10-30
ENA first public
ERC000011
ENA-CHECKLIST
UOM-BCF
INSDC center name
public
INSDC status
ERS24548527
SRA accession
E-MTAB-15136:Sample 18
Submitter Id
ArrayExpress
broker name
not collected
collection date
Protocols: Three Maudiozyma bulderi strains used in this study CBS 8638, CBS 8639, and NRRL Y-27205 were obtained from the Agricultural Research Service (ARS-NRRL) culture collection. The yeasts were cultured and maintained on YPD agar medium (15 g/L agar, 10 g/L yeast extract, 20 g/L peptone, 20 g/L glucose) or in SD minimal media (Yeast nitrogen base with ammonium sulphate and amino acids 6.7g/L)  Bioreactor fermentations for RNA extraction were conducted using one litre stirred tank bioreactors (Multifors, Infors-HT, Bottmingen, Switzerland). All fermentation experiments were carried out with cells grown in 500 mL of SD minimal media supplemented with 20g/l glucose. Fermentations were inoculated with cells from YPD overnight culture, washed twice in sterile deionised water, to achieve an initial optical density (OD) of 0.1. Three replicates of each strain were then cultured in 500 mL of YNB supplemented with 20g/l glucose and adjusted to either pH 5.5 or 2.5 with H2SO4. The pH was maintained at 5.5 and 2.5 using either 10 M NaOH or 1 M H3PO4 for pH adjustment. Temperature was maintained at 25°C, with agitation set at 300 rpm. For RNA extraction, 10-20 mL of cells with OD between 0.7 and 1.0 were harvested and promptly snap-frozen with liquid nitrogen.  Total RNA was extracted from 1x10^7 cells of three biological replicates harvested at the logarithmic growth phase (OD600 0.5-1.0) using the RNeasy Mini Kit (QIAGEN, Germany) following the manufacturer’s protocol for enzymatic digestion of the cell wall followed by lysis of spheroplasts. The concentration of lyticase was optimized to 50U per 107 cells for efficient cell lysis. To eliminate genomic DNA contamination, an additional DNase treatment was performed using the RNase-free DNase set (QIAGEN, Germany) according to the manufacturer’s instructions. The extracted RNA was quantified using a NanoDrop Lite Spectrophotometer (Thermo Fisher Scientific, United States).  Libraries were prepared from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc.) following the manufacturer’s instructions.
description
not collected
geographic location (country and/or sea)
not applicable
isolate
Maudiozyma bulderi
organism
Maudiozyma bulderi
organism
2.5
pH regimen
Maudiozyma bulderi
scientific_name
CBS8639
strain
Sample 18
title