|
| Status |
Public on Jul 18, 2014 |
| Title |
traductome PSI+ rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
ribosome protected fragments
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: 74D694
isogenic variation: PSI+
|
| Treatment protocol |
Cells are treated with cycloheximide
|
| Growth protocol |
OD600 of 0.6-0.8 at 30°C in YPD medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
As previously published by Ingolia et al, Science 324, 218-223 (2009).
Directional RNA-Seq library preparation was carried out with the Small RNA Sample Prep Kit and the v1.5 sRNA 3' Adaptor (Illumina), according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
polysome
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence unsing perl script
Unique mapping using Bowtie v0.12.7 with parameters -q -S -m 1 –un (unique mapping mode)
Measuring differential gene expression by assigning reads with Htseq-count version 0.5.3p3 using intersection-nonempty mode
Differential expression analysis with DESeq version 1.6.1 using default parameters
Genome_build: sacCer2
Supplementary_files_format_and_content: Count file from HTseq-count and differential gene expression file
|
| |
|
| Submission date |
Oct 15, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Olivier Namy |
| E-mail(s) |
olivier.namy@i2bc.paris-saclay.fr
|
| Organization name |
CNRS, Université Paris-Sud
|
| Department |
I2BC
|
| Lab |
Genomic, structure and Translation
|
| Street address |
Rue Gregor Mendel, bat 400
|
| City |
Orsay |
| ZIP/Postal code |
91400 |
| Country |
France |
| |
|
| Platform ID |
GPL13272 |
| Series (1) |
| GSE41590 |
Genome-wide translational changes induced by the prion [PSI+] |
|
| Relations |
| SRA |
SRX196433 |
| BioSample |
SAMN01766982 |
