|
| Status |
Public on Jan 01, 2018 |
| Title |
Wild type rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Wild type
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: Wild type
cultivated at: 25°C
temperature shift: 1h 37 °C
|
| Treatment protocol |
1h 37°C
|
| Growth protocol |
over night at 25 °C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were harvested at 1*10^7 cells/ml after 1h 37 °C, total RNA was extracted with Macherey-Nagel nucleospin RNA extraction Kit
RNA-samples were prepared with the "TruSeq RNA Sample Prep Kit v2" according to the manufacturer's protocol (Illumina). Single read (50 bp) sequencing was conducted using a HiSeq 2000 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalling and adapter trimming has been performed using Illumina's bcl2fastq v2.17
Reads were aligned to the S. cerevisiae genome (assembly R64-1-1) using STAR 2.5 and up to 2 mismatches in 50 bp.
Counting of reads mapping to intronic or exonic regions was performed using the featureCounts software with annotation from Ensembl. Intronic region annotation was downloaded from UCSC using the table browser and converted to GTF exon annotation format.
Normalization of read counts and differential expression analysis was conducted with the DeSeq2 package (v1.8.2)
Candidates for differential intron usage were identified by comparing the exon-/intron-specific fold change information.
Genome_build: R64-1-1 (GCA_000146045.2)
Supplementary_files_format_and_content: count files were generated with featureCounts as described above and processed with awk to contain tab-delimited exon-/intron-specific raw read counts
|
| |
|
| Submission date |
Jan 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
[email protected]
|
| Organization name |
Universitaetsmedizin Goettingen
|
| Department |
Department of Pathology
|
| Lab |
NGS Integrative Genomics
|
| Street address |
Kreuzbergring 57
|
| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE93307 |
Splicing defects in RNA export receptor mutants |
|
| Relations |
| BioSample |
SAMN06212480 |
| SRA |
SRX2480231 |
