|
| Status |
Public on Jun 28, 2017 |
| Title |
Riboseq_drpl6a_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
drpl6a
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rpl6a::kanMX4
|
| Treatment protocol |
For ribosome profiling cells were treated with cycloheximide 100ug/ml for 1 minute.
|
| Growth protocol |
Yeast was grown on YPD (1% yeast extract, 2% peptone and 2% glucose) medium at 30°C, 200 rpm unless otherwise stated. The cells were collected in mid-log phase at OD600 0.4-0.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A yeast cell pellet was resuspended in 1 ml of lysis buffer from Dynabeads® mRNA DIRECTTM Kit (61011, Life technologies) and lysed at 4°C with 1 volume of acid washed glass beads in a FastPrep instrument (Thermo Scientific) using 2 cycles with the following settings; 45 s at 6.5 speed with 3 min pause on ice between each cycle.
Libraries for mRNA sequencing were prepared using the “directional mRNAseq sample preparation” protocol from Illumina with minor modifications. Polysome profiling and sequencing of ribosome-protected mRNA fragments were performed according to protocol described in (Nedialkova and Leidel, 2015).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpl6a::kanMX4
rpko_expression_profiles.csv
rpko_ribseq_counts.csv
|
| Data processing |
Library strategy: Ribo-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to transcriptome based on the CDS annotations from the yeast database (http://www.yeastgenome.org) and the 5’/3’UTR mappings from Ref. (Nagalakshmi et al., 2008) using segemehl v0.1.7-411 with parameters --accuracy 90
Transcript counts were calculated based on uniquely mapped reads and used to estimate differential expression by DESeq2. Ribosome density foldchange was calculated using the ratio Riboseq foldchange by mRNAseq foldchange.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include read counts and fold-change for each strain
|
| |
|
| Submission date |
Aug 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joao C Guimaraes |
| E-mail(s) |
joaoguima@gmail.com
|
| Organization name |
University of Basel
|
| Department |
Biozentrum
|
| Street address |
Klingelbergstrasse 50 / 70
|
| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19756 |
| Series (2) |
| GSE85590 |
The Gcn4 Transcription Factor Reduces Protein Synthesis Capacity and Extends Yeast Lifespan [RNA-Seq] |
| GSE85591 |
The Gcn4 Transcription Factor Reduces Protein Synthesis Capacity and Extends Yeast Lifespan |
|
| Relations |
| BioSample |
SAMN05574562 |
| SRA |
SRX2022870 |
