|
Status |
Public on Dec 07, 2023 |
Title |
SPT16 GAL1pr-FLO8-sfGFP grown at 28C in galactose |
Sample type |
SRA |
|
|
Source name |
Mata his3200 leu21 lys2-128 ura3-52 trp163 NAT:GAL1pr-FLO8-sfGFP-HpH
|
Organism |
Saccharomyces cerevisiae S288C |
Characteristics |
strain: S288C treatment: grown at 28C in galactose
|
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
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|
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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 |
SAMN38710456 |
SRA |
SRX22811149 |