|
| Status |
Public on Aug 08, 2012 |
| Title |
ZK2_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Yeast S. cerevisiae strain ZK2
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: ZK2
application: Bioethanol strain
|
| 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 was extracted at early-stationary phase by the hot phenol method and then treated with RNase-free DNase I (TaKaRa) for 30 min according to the manufacturer’s protocols. The poly (A) containing mRNA molecules were purified and the cDNA libraries were prepared according to the manufacturer’s instructions (Illumina). The cDNA library products were sequenced on the Illumina HiSeq™ 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
After reads containing sequencing adapters and reads of low quality (those in which the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) were removed, the clear reads were aligned to the S. cerevisiae S288c genes (the sequences and the annotations of S. cerevisiae genes were downloaded form SGD database) with SOAPAligner. Mismatches no more than 2 bases were allowed in the alignment. The gene expression level was normalized by per kilobase of exon region per million mapped reads (RPKM). Gene coverage is the percentage of a gene covered by reads. This value is equal to the ratio of the base number in a gene covered by unique mapping reads to the total bases number of that gene.
Genome_build: sacCer2
|
| |
|
| Submission date |
Jul 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Daoqiong Zheng |
| E-mail(s) |
zhengdaoqiong@163.com
|
| 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 (1) |
| GSE31601 |
Transcription profile analysis of S. cerevisiae strains |
|
| Relations |
| SRA |
SRX171208 |
| BioSample |
SAMN01095768 |
