|
| Status |
Public on Oct 08, 2019 |
| Title |
IMX1939_Mtt2 |
| Sample type |
SRA |
| |
|
| Source name |
Shake flask mid exponential phase
|
| Organism |
Saccharomyces eubayanus |
| Characteristics |
carbon source: Maltotriose
strain: IMX1939
genotype phenotype: MATa/MATα Semalt1Δ/Semalt1Δ Sesga1Δ::ScMAL13/ Sesga1Δ::ScMAL13
|
| Treatment protocol |
S. eubayanus CDFM21L.1, IMX1765, IMX1939 and S. cerevisiae X S. eubayanus HTS020 were grown in either SMG or SMMal or SMMtt until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.
|
| Growth protocol |
S. eubayanus and S. cerevisiae X S. eubayanus batch cultures were grown on synthetic medium (SM) containing 3.0 g L-1 KH2PO4, 5.0 g L-1 (NH4)2SO4, 0.5 g L-1 MgSO4, 7 H2O, 1 mL L-1 trace element solution, and 1 mL L-1 vitamin solution. The pH was set to 6 with 2 M KOH prior to autoclaving at 120 °C for 20 min. Vitamin solutions (Verduyn et al. 1992) were sterilized by filtration and added to the sterile medium. Concentrated sugar solutions were autoclaved at 110 °C for 20 min and added to the sterile flasks to give a final concentration of 20 g L-1 carbon source (glucose (SMG), maltose (SMM)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The resulting ice pellet was gently thawed on ice and spun down at 4700 x g for 5 min at 0 o C. Pellets were then resuspended in 1.2 mL of ice-cold AE buffer (50 mM sodium acetate and 10 mM EDTA, pH 5.0), followed by addition of 1.2 mL of acid phenol/chloroform/isoamyl alcohol mix and 0.12 mL 10 % sodium dodecyl sulfate. The resulting mix was vortexed for 30 s and incubated for 5 min at 65 °C. After homogenizing for 30 sec by vortexing, 800 µL aliquots were distributed in RNase-free screw-cap tubes (Tai et al. 2005). After centrifugation (15 min at 10,000 x g), the aqueous phase was transferred to a new tube containing 0.4 mL of acid phenol/chloroform. The mix was vortexed for 30 seconds, centrifuged (15 min at 10,000 x g) and the aqueous phase was again transferred to a new tube. RNA was then ethanol precipitated and re-suspended in RNAse-free water. Prior to cDNA synthesis, purity, concentration and integrity of the RNA in the samples was assessed with the Nanodrop (Thermo Fisher Scientific), Qubit (Thermo Fisher Scientific) and Tapestation 220 with RNA Screen Tape (Agilent Technologies), respectively, according the manufacturers’ recommendations.
cDNA libraries were prepared using the TruSeq RNA V2 kit (Illumina)and sequenced on HISeq 2500 (Illumina) at Novogene (HK) Company Ltd (Hong Kong, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
S. eubayanus IMX1939 was grown in SMMtt until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.
|
| Data processing |
RNA-Seq reads were aligned to CDFM21L.1 or to a hybrid CDFM21L21.1-CBC-1 reference using STAR version 2.5.3a in 2Pass mode
resulted sequence alignment map file (SAM) were filtered on ambigious alignments and sorted with samtools to sorted binary alignement file (BAM)
The sorted BAM file was processed with featureCounts from the SubRead package version1.6.3 with -M and -s 1 for stranded reverse to calculate the transcript counts
The raw transcript counts were normalized on fragments per kilobase million (FPKM) by applying rpkm module from edgeR package
Genome_build: CDFML21L.1 and CBC-1 this study,
Supplementary_files_format_and_content: Comma delimited file, normalized transcript counts
|
| |
|
| Submission date |
Jun 21, 2019 |
| Last update date |
Oct 09, 2019 |
| Contact name |
Jean-Marc Daran |
| E-mail(s) |
j.g.daran@tudelft.nl
|
| Phone |
+31 15 278 2412
|
| Organization name |
Delft University of Technology
|
| Department |
Department of Biotechnology
|
| Lab |
Kluyver centre for genomics of industrial organisms
|
| Street address |
Julianalaan 67
|
| City |
Delft |
| ZIP/Postal code |
2628BC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL25341 |
| Series (1) |
| GSE133146 |
Maltotriose consumption by hybrid Saccharomyces pastorianus is heterotic and results from regulatory cross-talk between parental sub-genomes |
|
| Relations |
| BioSample |
SAMN12107530 |
| SRA |
SRX6102491 |
