|
| Status |
Public on Apr 12, 2023 |
| Title |
glycerol, T=15 (pH 8.0), rep 3 [a2] |
| Sample type |
SRA |
| |
|
| Source name |
whole cell
|
| Organism |
Komagataella phaffii |
| Characteristics |
tissue: whole cell
cell line: X-33
genotype: wild type
growth condition: glycerol, T=15 (pH 8.0)
|
| Treatment protocol |
For the analysis of the transcriptional response of K. phaffii to alkalinization of the medium cells were grown overnight on YPD or YPGly medium, and then cultures were diluted in 200 ml of fresh medium at OD600=0.2 and grown until the OD600 of the cultures reached around 0.6. Then two 100 ml-aliquots were centrifuged (5 min at 1000xg). One aliquot was resuspended in the same volume of either fresh YPD or YPGly medium plus 50 mM TAPS pH 5.5 (control cells) or in YPD or YPGly supplemented with 50 mM TAPS adjusted to pH 8.0 or 8.2 (stressed cells). Samples (15 ml) were taken immediately after resuspension in medium at pH 5.5 (time=0) and, for each stressed culture, after 15, 30 and 60 min. In all cases samples were placed on ice and immediately centrifuged at 4 °C.
|
| Growth protocol |
K. phaffii X-33 was grown at 28 °C in YP medium (10 g/L yeast extract, 20 g/L peptone) supplemented with a 20 g/L of glycerol (YPGly) or glucose (YPD).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Ribo Pure™-Yeast kit (Ambion) following the manufacturer’s instructions. The quality was assessed by capillary electrophoresis in a Bioanalyzer equipment and RNA amounts quantified by measuring the A260 in a Nanodrop ND-1000 Spectrophotometer.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP (non-directional library). The library was checked by Qubit™ assay (Thermofisher) and real-time PCR for quantification and size distribution monitored with a Bioanalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GlyT15-pH8 rep3
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx
|
| Data processing |
Mapping of fastq files to generate SAM files was carried out with the Bowtie2 software (Langmead & Salzberg, 2012) in local / sensitive mode against the GCA_000027005.1 assembly (98.4–99.2% mapped reads). The SeqMonk software v1.48.0 (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) was employed to analyze the SAM files. Mapped reads were counted using the RNA-Seq pipeline on mRNA features and differentially expressed genes with respect to time zero were identified using the built-in DESeq2 R package
Assembly: GCA_000027005.1
Supplementary files format and content: file "Annotated Probe Report for All Probes_RPKM.xlsx", excel file with "Reads Per Kilobase Million" data for each sample.
Supplementary files format and content: file "supplemental Table 2.xlsx", excel file conaining the diferentially expressed genes for each condition as defined by the DESeq2 R package (fold-change log2 >1 or <-1 and p-value < 0.01) plus functional annotations
|
| |
|
| Submission date |
Feb 03, 2023 |
| Last update date |
Apr 12, 2023 |
| Contact name |
JOAQUIN ARINO |
| E-mail(s) |
joaquin.arino@uab.es
|
| Organization name |
UNIVERSITAT AUTONOMA BARCELONA
|
| Department |
Biochemistry & Mol. Biol.
|
| Lab |
Yeast Molecular Biology
|
| Street address |
ED. IBB
|
| City |
CERDANYOLA DEL VALLES |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL27930 |
| Series (1) |
| GSE224427 |
Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization |
|
| Relations |
| BioSample |
SAMN33051934 |
| SRA |
SRX19272669 |
