|
| Status |
Public on Dec 07, 2023 |
| Title |
spt16-197 FLO8-sfGFP grown at 37C in dextrose |
| Sample type |
SRA |
| |
|
| Source name |
Mata his3200 leu21 lys2-128 ura3-52 trp163 FLO8-sfGFP-HpH spt16-197
|
| Organism |
Saccharomyces cerevisiae S288C |
| Characteristics |
strain: S288C
treatment: grown at 37C in dextrose
|
| Treatment protocol |
Cells were grown in either dextrose or galactose at 28 or 37C for one hour.
|
| Growth protocol |
Cells were grown in yeast extract, peptone media to mid-log phase.
|
| Extracted molecule |
other |
| Extraction protocol |
Total RNA was isolated using hot acid phenol from 10 OD600 units of cells.
rRNA depletion and library preparation was performed by Azenta Life Sciences .
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
other |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FASTQ files were mapped to custom Saccer3 genomes with the FLO8::sfGFP alleles using BWA-MEM.
Mapped reads were filtered for MAPQ score >10, sorted, and reads mapping to chrV extracted using Samtools view.
BAM files were converted to strand-specific wig files using the BAM to Wiggle tool in Galaxy (Version 5.0.1+galaxy2), and normalized to reads per genome coverage using the Java Genomics Toolkit. (https://github.com/timpalpant/java-genomics-toolkit) wigmath.Scale.
Assembly: saccer3_FLO8_crypTSS_sfGFP.fa (YLH1086 and YLH1088) and saccer3_GAL1pr_FLO8_crypTSS_sfGFP.fa (YLH2036)
Supplementary files format and content: wig files with reads from chrV and normalized to reads per genome coverage
|
| |
|
| Submission date |
Dec 07, 2023 |
| Last update date |
Dec 07, 2023 |
| Contact name |
LeAnn Howe |
| E-mail(s) |
ljhowe@mail.ubc.ca
|
| Phone |
6048226297
|
| Organization name |
University Of British Columbia
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
2350 Health Sciences Mall
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL33992 |
| Series (2) |
| GSE249580 |
A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae [RNA-seq] |
| GSE249628 |
A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae |
|
| Relations |
| BioSample |
SAMN38710458 |
| SRA |
SRX22811147 |
