|
| Status |
Public on Jan 03, 2024 |
| Title |
Ribo WT+SM replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cell
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell type: yeast cell
genotype: WT
strain: BY4742 (MAT{alpha} his3{delta}1 leu2{delta}0 lys{delta}2 ura3{delta}0)
treatment: SM
|
| Treatment protocol |
Cells were treated with the antimetabolite Sulfometuron methyl (SM) at 1 µg/mL for 25 before harvesting.
|
| Growth protocol |
Yeast cells were generally grown to an OD600 of 0.5-0.6 in synthetic complete medium lacking isoleucine and valine (SC-Ilv) at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "eIF1A residues implicated in cancer stabilize translation preinitiation complexes and favor suboptimal initiation sites in yeast" Martin Marcos et al. (2017) eLife 6:e31250
Ribosome-protected RNA 25-34 nt
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
DESeq2 WT+SM vs WT.xlsx and DESeq2 eIF2Adelta+SM vs WT+SM.xlsx
|
| Data processing |
For ribo-seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. Subsequently, rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq samples, the same protocol mentioned above for ribo-seq analysis was followed.
Translational efficiency change analysis was performed with R DESeq2 package.
Assembly: sacCer3
Supplementary files format and content: The DESeq2 files to represent fold-change and raw reads that were used as input for the fold-change analysis
Library strategy: Ribo-seq
|
| |
|
| Submission date |
Aug 22, 2023 |
| Last update date |
Jan 03, 2024 |
| Contact name |
Swati Gaikwad |
| Organization name |
National Institutes of Health
|
| Department |
Section on Nutrient Control Of Gene Expression
|
| Lab |
Hinnebusch, Alan
|
| Street address |
Building 6, Room 233
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-2716 |
| Country |
USA |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE241473 |
Yeast eIF2A plays a minimal role in translation initiation in vivo |
|
| Relations |
| BioSample |
SAMN37116719 |
| SRA |
SRX21459039 |
