|
| Status |
Public on May 10, 2019 |
| Title |
RNA-seq Nrd1-AA_drpd3_-Rap_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
RNA-seq Nrd1-AA_drpd3_-Rap
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: HHY168
genotype/variation: Nrd1-AA drpd3
treatment: Minus Rapamycin 1h (1μg/ml)
|
| Treatment protocol |
With or without 1μg/ml of rapamycin for 1h
|
| Growth protocol |
All strains were derived from the Anchor-Away genetic backgrounds (Haruki et al. 2008). Cells were grown in YEPD medium (1% yeast extract, 1% peptone) supplemented with 2% glucose as carbon source. All strains were grown at 30°C and were not affected in growth by the different tags or deletions. Anchor-away of Nrd1-AA was induced by adding 1μg/ml of rapamycin to the medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using Glass-beads and TRIzol (Invitrogen).
ribodep stranded RNA (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
NOTE: processed data was generated from both rep1 & rep2, and is linked to the corresponding rep1 sample records.
|
| Data processing |
Single-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009) with options '-k 20 --end-to-end --sensitive -X 800'. PCR duplicates were removed from the analysis. BigWig coverage files were generated using Bam2wig function. Differential expression analysis was performed using the R/Bioconductor package DEseq on mRNA annotations Ensembl (Saccharomyces_cerevisiae.EF4.65.gtf).
Genome_build: saccer3
Supplementary_files_format_and_content: bigWig files of Watson and Crick Strands. Each file corresponds to the mean of rep1 and rep2.
|
| |
|
| Submission date |
May 09, 2019 |
| Last update date |
May 10, 2019 |
| Contact name |
Julien Soudet |
| E-mail(s) |
julien.soudet@unige.ch
|
| Organization name |
Université de Genève
|
| Department |
BICEL
|
| Street address |
30 quai Ansermet
|
| City |
Geneva |
| ZIP/Postal code |
1204 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE130946 |
Fine chromatin-driven mechanism of transcription interference by antisense noncoding transcription |
|
| Relations |
| BioSample |
SAMN11609480 |
| SRA |
SRX5811076 |
