|
Status |
Public on Sep 22, 2021 |
Title |
lem2_RNA-seq_rep8 |
Sample type |
SRA |
|
|
Source name |
logarithmically growing lem2-delta cells
|
Organism |
Schizosaccharomyces pombe |
Characteristics |
strain: lem2-delta 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 lem2∆ 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 |
SAMN21540978 |
SRA |
SRX12286301 |