|
| Status |
Public on Jul 28, 2021 |
| Title |
G14_28_2 |
| Sample type |
SRA |
| |
|
| Source name |
cell pellet
|
| Organism |
Komagataella phaffii GS115 |
| Characteristics |
genotype: oxidative and thermal stress cross-tolerant mutant
treatment: induction temperature 28 degrees C
time: 60h
|
| Treatment protocol |
Induction temperature: 28℃ and 37℃
|
| Growth protocol |
Flask-batch fermentation in BMGY/BMMY medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
G14_28_2
|
| Data processing |
Illumina Casava software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCA_000223565.1/
|
| |
|
| Submission date |
Feb 20, 2021 |
| Last update date |
Jul 28, 2021 |
| Contact name |
Nai-Xin Lin |
| E-mail(s) |
[email protected]
|
| Organization name |
Jiangnan University
|
| Street address |
lihu avenue
|
| City |
Wuxi |
| ZIP/Postal code |
214122 |
| Country |
China |
| |
|
| Platform ID |
GPL29747 |
| Series (1) |
| GSE167141 |
Gene expression levels of evolved thermotolerant yeast and its parent under fermentation condition |
|
| Relations |
| BioSample |
SAMN18015616 |
| SRA |
SRX10141730 |
