|
| Status |
Public on Feb 02, 2018 |
| Title |
arp5-1 |
| Sample type |
SRA |
| |
|
| Source name |
arp5KO
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: BY4741
genotype: BY4741 arp5::LEU2
growth protocol: Yeast liquid culture
|
| Treatment protocol |
Asynchronous culture was treated with 30 nM rapamycin for 45 min, 90 min, or was untreated
|
| Growth protocol |
Yeast were grown to mid-log-phase in YPD medium at 30C. (Asynchronous culture).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pellets were collected, snap-frozen and then processed as per the RNA-seq protocol outlined. Two biological replicates were collected(-1,-2 or -3,-4 or -5,-6). RNA was prepared from samples (approximately 1.5 ODs) using the MasterPure™ Yeast RNA Purification Kit (Epicentre, MPY03100).
The sequencing libraries were prepared from 0.8 µg of RNA/sample using the Illumina TruSeq Stranded mRNA kit (Illumina, 15031047). The quality of the pooled library was checked using the Agilent Bioanalyser 2100 HS DNA assay. The library was sequenced on an Illumina HiSeq 2000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
arp5KO Untreated rep1
|
| 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 |
Sep 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sean Beckwith |
| Organization name |
Stanford University
|
| Department |
Biology
|
| Lab |
Morrison Lab
|
| Street address |
371 Serra Mall
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE103468 |
Genetic dissection of chromatin regulators reveals the INO80 chromatin remodeling complex as a key metabolic regulator utilizing TORC1 and histone acetylation pathways |
|
| Relations |
| BioSample |
SAMN07604745 |
| SRA |
SRX3159673 |
