|
| Status |
Public on Apr 30, 2024 |
| Title |
mex67-5 xpo1-1 cytoplasm rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Cytoplasmic fraction of cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
genotype: mex67-5 xpo1-1
condition: Shifted to 37C for 1h
cell fraction: Cytoplasmic
|
| Treatment protocol |
Shifted to 37°C for 1h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NucleoSpin® RNA; Macherey-Nagel.
Non-stranded mRNA Seq TruSeq standard according to the Illumina protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.17.1.14.
STAR version 2.5.2a was used to align the reads to the sacCer3 genome using 2 mismatches within 50 bases.
featureCounts version 1.5.0-p1 was used to quantify reversely-stranded reads (-s 2) for genes in sacCer3 version 68.
Genome_build: sacCer3 version 68
Supplementary_files_format_and_content: *_geneCounts.txt: Tab-delimited text files include gene counts.
Supplementary_files_format_and_content: *.gtf: The annotation of the aligned files was performed using a custom GTF.
|
| |
|
| Submission date |
Nov 08, 2021 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
|
| 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 |
GPL21656 |
| Series (1) |
| GSE188455 |
Double-stranded RNA formation leads to preferential nuclear export and gene expression |
|
| Relations |
| BioSample |
SAMN22999592 |
| SRA |
SRX13075963 |
