|
| Status |
Public on Jul 08, 2017 |
| Title |
MJE7_Rap_for_NC2baa_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
WT
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: MJE7 Background
|
| Treatment protocol |
Add rapamycin to 8 ug/ml and treat for 24 hours, keep in log phase by dilution during treatment.
|
| Growth protocol |
Overnight incubated yeast cells were diluted in YPD and grow to exponential phase. Add rapamycin to 8 ug/ml and treat for 24 hours, keep in log phase by dilution during treatment.
Overnight incubated yeast cells were diluted in YPD and grow to exponential phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with phenol, digested with DNase and further purified by Trizol
Total RNA was extracted with phenol, digested with DNase and further purified by Trizol
Libraries of mRNA were prepared with KAPA stranded mRNA-Seq Kits v2 following the manufacturer’s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
in YPD
Sample 72
|
| Data processing |
For yeast mRNA-seq
Fastq files were used to map reads to yeast genome(saccer3) with TopHat v2.0.8 (for FPKM analysis, treat as single end)
Caclutate FPKM using accepted bam file from cuffdiff cuffdiff v2.0.2 for mRNA-Seq
mapped reads(sam file) were used to cacullate the mRNA level and log2 ratio of mutants vs WT using customed script
log2 ratio of mutants vs wt were used to plot with metagene profiles.
genome build: sacCer3
|
| |
|
| Submission date |
Jun 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Siavash K Kurdistani |
| E-mail(s) |
Skurdistani@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Lab |
Kurdistani
|
| Street address |
615 Charles E Young Dr South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE95633 |
MINC Regulates Pervasive Transcription in Yeast and Mammals |
|
| Relations |
| BioSample |
SAMN07204573 |
| SRA |
SRX2894809 |
