|
| Status |
Public on Oct 10, 2012 |
| Title |
ZTW1 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Yeast S. cerevisiae strain
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: ZTW1, a Wild type strain
application: Bioethanol strain
|
| Treatment protocol |
mRNA is extrated when yeast cells enter the early-stationary phase.
|
| Growth protocol |
Yeast cells were cultured in 25mL YPD medium (10g/L yeast extract, 20g/L peptone, and 20g/L glucose) with an initial OD600 of 0.05.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA of every sample was extracted using hot phenol method and then treated with RNase-free DNase I (TaKaRa) for 30 min according to the manufacturer’s protocols. The concentration and integrity of total RNA was checked using Agilent Technologies 2100 Bioanalyzer. The poly (A) containing mRNA molecules were then purified and the cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
After removing reads containing sequencing adapters and reads of low quality (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read), the clear reads were aligned to the S. cerevisiae S288c genes (ftp://ftp.ncbi.nih.gov/genomes/Fungi/Saccharomyces_cerevisiae_uid128) and genes using SOAPAligner.Mismatches no more than 2 bases were allowed in the alignment.
Genome_build: sacCer2
Supplementary_files_format_and_content: rpkm
|
| |
|
| Submission date |
Sep 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Daoqiong Zheng |
| E-mail(s) |
[email protected]
|
| Phone |
86 571 88206636
|
| Organization name |
College of Life Sciences, Zhejiang University
|
| Department |
Institute of Microbiology
|
| Street address |
866 Yuhangtang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE40905 |
Transcription profile analysis of S. cerevisiae ZTW1 wild-type and mutant strains |
| GSE41017 |
Comparison of the genomic structures and transcription between S. cerevisiae strains ZTW1 and ZGR3 |
|
| Relations |
| SRA |
SRX187114 |
| BioSample |
SAMN01176879 |
