|
| Status |
Public on Jun 17, 2024 |
| Title |
SpIB2 lager yeast, day 5, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SpIB2 lager yeast
|
| Organism |
Saccharomyces pastorianus |
| Characteristics |
strain: SpIB2 lager yeast
time: Day 5
|
| Growth protocol |
Both strains were inoculated in standar brewing wort and Fermentation proceeded for five days at 16°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For total RNA extraction, the hot phenol protocol was performed. the RNA integrity number (RIN) above 8 was used for the preparation of sequencing libraries.
RNA libraries was prepared at GENEWIZ and the Poly-A selection was done to capture only mRNA species.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Transcriptomic paired-end reads for both yeast strains were quality-trimmed using Trimmomatic version 0.38 with the parameters LEADING:5 TRAILING:5 MINLEN:50 and Sortmerna for contaminant RNA removal
Trimmed sequence reads were mapped to Saccharomyces pastorianus CBS1418 GCA_011022315.1 refernece genome with STAR software version 2.7.3a with the default parameters
Raw read count calculation was done with HTSeq-count version 0.11.1
The differential gene expression analyisis was done with edgeR version 3.34.0
Assembly: GCA_011022315.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
|
| |
|
| Submission date |
Jun 14, 2024 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Benito Pereyra Alférez |
| E-mail(s) |
benito.pereyraal@uanl.edu.mx, cesar.hernandezvsqz@uanl.edu.mx
|
| Organization name |
Universidad Autónoma de Nuevo León
|
| Department |
Instituto de Biotecnología
|
| Lab |
Laboratorio 4
|
| Street address |
Av. Pedro de Alba S/N
|
| City |
San Nicolás de los Garza |
| State/province |
Nuevo León |
| ZIP/Postal code |
66455 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL34596 |
| Series (1) |
| GSE269873 |
Expression Patterns of Mal genes and Association with Differential Maltose and Maltotriose Transport rate of Two Saccharomyces pastorianus Yeasts |
|
| Relations |
| BioSample |
SAMN41839018 |
| SRA |
SRX24927278 |
