|
| Status |
Public on May 29, 2024 |
| Title |
IST536 MM15 cells, exponential, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Rhodotorula toruloides |
| Characteristics |
cell type: yeast
genotype: Evolved strain
|
| Growth protocol |
Cells grown in minimal medium (2% glucose, 0.69% YNB)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed by using a modified hot phenol method, described in Amin-ul Mannan et., Analytical Biochemistry, (2009), and then purified using the commercial kit RNA Clean & Concentrator-5 (Zymo Research)
RNA libraries preparations were carried out by Novogene Bioinformatics Technology for Illumina sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads containing adapter sequences, containing poly-N, or low quality reads were removed from raw data using Trimmomatic
Paired-end clean reads were aligned using HISAT2 v2.2.0 (--phred33 --dta)
read count was performed using featureCounts from the Subread package v2.0.4
Differential expression analysis was performed using the DESeq2 R package v1.42.0
Assembly: GCA_963855905 (not public yet)
Supplementary files format and content: tab-delimited text files include the output from DESeq2
|
| |
|
| Submission date |
Jan 26, 2024 |
| Last update date |
May 29, 2024 |
| Contact name |
Isabel Sá-Correia |
| E-mail(s) |
[email protected]
|
| Organization name |
Instituto Superior Técnico
|
| Department |
Department of Bioengineering
|
| Lab |
iBB-Institute for Bioengineering and Biosciences
|
| Street address |
Avenida Rovisco Pais, 1
|
| City |
Lisbon |
| ZIP/Postal code |
1049-001 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL32811 |
| Series (1) |
| GSE254308 |
Transcriptional profiling of Rhodotorula toruloides IST536 and derived evolved strain IST536 MM15 under non-stressing conditions |
|
| Relations |
| BioSample |
SAMN39620680 |
| SRA |
SRX23408317 |
