|
| Status |
Public on Nov 26, 2022 |
| Title |
111419 npl3- F245I (2) 37c |
| Sample type |
SRA |
| |
|
| Source name |
whole cell RNA extract
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: W303, npl3-shuffle, pRS315-npl3-F245I
treatment: 37°C 1 hour
genotype: MATa, ura3-1, trp1-1, his3-11,15, leu2-3,112, ade2-1, can1-100, GAL+
|
| Growth protocol |
overnight cultures were diluted to OD600 = 0.2 and kept growing in YPD at 30°C for ~4 hours till they reached mid-log phase. Cells with treatment were shifted to a shaking water bath at 37°C for 1 hour when reached mid-log phase before 10 ml culture was pelleted
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extraced from cell pellet of 10 ml mid-log phase grown cells using Trizol reagent (Invitrogen) and used according to manufactures protocol
Illumina TruSeq mRNA stranded; handled according to the manufacturer’s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For all genomic analyses, Saccharomyces cerevisiae S288c genome and gene annotation assembly (version R64-1-1) were downloaded from the EnsemblFungi database (https://fungi.ensembl.org/index.html). The annotation file was edited to replace all "transcript" entries with "Parent" and all "gene" entries with "ID". After initial quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), RNA-seq reads were mapped using the splice-aware alignment tool STAR (version 2.7.2a) with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04. Reads were counted into exons using HTSeq-count from the HTSeq Python package. The following parameters were set: --stranded reverse --order pos --idattr ID --type exon.
|
| |
|
| Submission date |
Nov 03, 2020 |
| Last update date |
Nov 26, 2022 |
| Contact name |
Kathi Zarnack |
| E-mail(s) |
kathi.zarnack@bmls.de
|
| Organization name |
Goethe University Frankfurt
|
| Department |
Buchmann Institute for Molecular Life Sciences (BMLS)
|
| Street address |
Max-von-Laue-Str. 15
|
| City |
Frankfurt |
| ZIP/Postal code |
60438 |
| Country |
Germany |
| |
|
| Platform ID |
GPL27812 |
| Series (1) |
| GSE160709 |
The SR-like protein Npl3 transfers mRNP components from the transcription site onto the mRNA |
|
| Relations |
| BioSample |
SAMN16634010 |
| SRA |
SRX9423633 |
