|
| Status |
Public on Jan 03, 2018 |
| Title |
RAP_TREAT_90min_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: BY4741
growth phase: Asynchronous culture
|
| Treatment protocol |
Asynchronous culture was treated in mid-log phase with 30 nM rapamycin for 90 minutes. Pellets were collected, snap-frozen and then processed as per the RNA-seq protocol outlined. Two biological replicates were collected (5 & 6).
|
| Growth protocol |
Yeast grown in continuous culture to induce metabolic cycling; samples taken at different times across these metabolic cycles. Samples A and B are replicates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
yeast were harvested and flash frozen. RNA was extracted using MasterPure RNA extraction kit (MPY03100).
0.8 µg of RNA was used with the Illumina TruSeq mRNA kit (15031047) using standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RAP_FPKM.csv
|
| Data processing |
Reads were aligned using Bowtie2 and analysed using DESeq2. Replicates were combined for analysis and genes with low reads (< 5 FPKM across all samples) were removed.
Genome_build: sacCer3 (April 2011)
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Jan 03, 2018 |
| Last update date |
Jan 08, 2018 |
| Contact name |
Graeme Gowans |
| E-mail(s) |
ggowans@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Biology
|
| Lab |
Ashby Morrison
|
| Street address |
Gilbert Building, 371 Serra Mall
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE101290 |
INO80 Chromatin Remodelling Coordinates Metabolic Homeostasis with Cell Division |
|
| Relations |
| BioSample |
SAMN08289389 |
| SRA |
SRX3529714 |
