|
| Status |
Public on Sep 22, 2021 |
| Title |
wt_RNA-seq_rep16 |
| Sample type |
SRA |
| |
|
| Source name |
logarithmically growing WT cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: WT
batch: h
|
| Growth protocol |
Standard conditions were used to produce logarithmically growing cultures in rich media (YES).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol
Library was constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB#E7420), according to manufacturer's recommendation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
RNA sequencing of WT cells
|
| Data processing |
Raw read were de-multiplexed. Adapter-trimmed reads were aligned to the S. pombe reference genome (ASM294v2.27) and a custom GTF file using STAR (v2.7.3a) and processed using RSEM (v1.3.3).
Differential expression was analysed using the DESeq2 (v1.22.2) and tximport (v1.10.1) R libraries.
Bedgraph coverage files were generated using genomecov (bedtools v2.29.1).
Genome_build: ASM294v2.27
Supplementary_files_format_and_content: Bedgraph files of coverage
|
| |
|
| Submission date |
Sep 21, 2021 |
| Last update date |
Sep 22, 2021 |
| Contact name |
Sigurd J Braun |
| Organization name |
LMU
|
| Department |
BMC
|
| Street address |
Großhaderner Str. 9
|
| City |
Planegg |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30658 |
| Series (1) |
| GSE174347 |
RNA surveillance and the periphery: a novel role for nuclear envelope protein Lem2 |
|
| Relations |
| BioSample |
SAMN21540981 |
| SRA |
SRX12286303 |
