|
| Status |
Public on Dec 19, 2023 |
| Title |
NuclearExtract_replicate2_stress_Nab2-IDRmutant |
| Sample type |
SRA |
| |
|
| Source name |
BY4742
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tissue: BY4742
condition: stress
genotype: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-{delta}QQQP-{delta}RGG({delta}104-263)-SV40NLS-yEGFP-HISMX
|
| Treatment protocol |
Cells were harvested in mid-log phase in medium with glucose (no-stress) or washed 3x in synthetic complete medium without glucose, and cultured for another 24 hrs in synthetic complete medium without glucose before harvesting (stress).
|
| Growth protocol |
Yeast cells were grown in synthetic complete medium with 2% glucose until mid-log phase.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
1) Whole cell extracts: Cells were harvested and snap-frozen in liquid N2. Pellets were resuspended in lysis buffer and further processed with acid-saturated phenol and chloroform to extract total RNA. Purified RNA was processed with Dynabeads with oligodT(25) for PolyA selection. 2) Nuclear extracts: Cells were spheroplasted with Zymolyase to remove cell walls. Nuclei were released in buffer containing 20% Ficoll and dounced to mechanically assist nucleus release. Nuclei were separated from remaining cell material/debris through sucrose gradient fractionation. The enriched nucleus fraction was resuspended in lysis buffer and further processed with acid-saturated phenol and chloroform to extract total RNA. Purified RNA was processed with Dynabeads with oligodT(25) for PolyA selection.
The eluted poly(A) RNA was used to generate strand-specific sequencing libraries using the NEXTflex Rapid Directional RNA-Seq Library Prep Kit (BioO)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
MZ_RNA_Seq_135
|
| Data processing |
Reads were adaptor trimmed using cutadapt, mapped to the reference genome using tophat2 after rRNA reads subtraction using botwtie2, and the read counts per gene were quantified using featurecount.
Assembly: The FASTA file of the Yeast Genome was downloaded from the Saccharomyces Genome Database "SGD"
Supplementary files format and content: text file containing the calculated read counts per gene.
|
| |
|
| Submission date |
Nov 15, 2023 |
| Last update date |
Dec 19, 2023 |
| Contact name |
Mostafa Zedan |
| E-mail(s) |
[email protected]
|
| Organization name |
ETH-Zurich
|
| Street address |
Otto-Stern-Weg 3
|
| City |
Zürich |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL31112 |
| Series (1) |
| GSE247953 |
Glucose stress causes mRNA retention in nuclear Nab2 condensates |
|
| Relations |
| BioSample |
SAMN38271813 |
| SRA |
SRX22541030 |
