|
| Status |
Public on Nov 18, 2016 |
| Title |
3.5h in SPO medium_IME1_IME4_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells_3.5h in SPO medium (IME1 IME4 induction)
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: strain A 33606
timepoint: 3.5h
|
| Treatment protocol |
cultured in SPO medium for 2 hours and 25mM CuSO4 is added to the culture to induce IME1 and IME4 expression to generate synchronized meiotic culture
|
| Growth protocol |
cells were grow in YPD plates and then YPD liquid medium to saturation. Diluted in BYTA medium overnight. Shifted into SPO medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA prepared by Ambion Ribopure Yeast Extraction kit (Am1926)
NuGen ovation universal RNA-seq system 1-96 (PN 0402-A01) primed with random hexamer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
self-written script for Basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome UCSC R64-1-1 (SacCer3) using bowtie 2v2.2.62
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks 2.2.1
Genome_build: UCSC R64-1-1 (SacCer3)
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample
|
| |
|
| Submission date |
Nov 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bruce Futcher |
| Organization name |
Stony Brook University
|
| Department |
Molecular Genetics & Microbiology
|
| Lab |
Life Sciences Building Rm363
|
| Street address |
STONY BROOK UNIVERSITY
|
| City |
Stony Brook |
| State/province |
NY |
| ZIP/Postal code |
11794-5222 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE90008 |
High throughput sequencing in synchronized yeast meiotic culture with pCUP1-IME1 pCUP1-IME4 strain |
| GSE90009 |
Synchronized yeast meiotic culture timecourse |
|
| Relations |
| BioSample |
SAMN06033687 |
| SRA |
SRX2357035 |
