|
| Status |
Public on Mar 01, 2024 |
| Title |
Scer, optimal growth, RNA, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
BJ5464 (delta-URA3)
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BJ5464 (delta-URA3)
treatment: Optimal growth
|
| Treatment protocol |
Splitting the culture into equal volumes, one underwent 37°C heat stress for 20 minutes.
|
| Growth protocol |
We grew Saccharomyces cerevisiae strain BJ5464 auxotroph ΔURA3 in 500 mL Yeast Extract-Peptone-Dextrose (YPD) medium to OD600 = 0.75 at 28°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
We resuspended three 2 mL aliquots per culture in 450 mL RLT Buffer and followed the manufacturer’s instructions for the Qiagen RNeasy plant mini kit, eluting in 30 mL nuclease-free water.
Illumina stranded mRNA library prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Genome preparation : We performed repeat masking with RepeatMasker v.4.1.0 (http://www.repeatmasker.org) through two rounds of masking, first with default settings and with standard Illumina adapters using -e rmblast enabled.
Alignment: We aligned RNA-Seq reads with kalign (ngskit4b tool suite version 200218) with options -c25 -l25 -d50 -U4. We removed PCR and optical duplicates using MarkDuplicates (PICARD) enabling REMOVE_DUPLICATES=TRUE.
FPKM: We calculated FPKM using the Tuxedo pipeline. We then z-transformed the FPKM values using the R package zFPKM.
edgeR: For the differential expression analyses, we used the Trinity edgeR pipeline to calculate log2FC between treatments.
Assembly: S288C R64/sacCer3
Supplementary files format and content: tab-delimited text file including FPKM for all samples
Supplementary files format and content: tab-delimited text file output from edgeR including logFC between treatments for each gene
|
| |
|
| Submission date |
Feb 20, 2024 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Erin Elizabeth Hahn |
| E-mail(s) |
erin.hahn@csiro.au
|
| Organization name |
CSIRO
|
| Department |
National Research Collections Australia
|
| Street address |
Clunies Ross
|
| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2611 |
| Country |
Australia |
| |
|
| Platform ID |
GPL27812 |
| Series (1) |
| GSE256160 |
Effects of formalin-fixation on FAIRE-Seq and MNase-Seq signatures in yeast (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN40008066 |
| SRA |
SRX23677965 |
