|
| Status |
Public on May 21, 2020 |
| Title |
shew_control |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Shewanella baltica |
| Characteristics |
strain: OS185
treatment: growth at 20C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Qiagen RNA Isolation kit according to the manufacturer's protocol.
RNA depleted of ribosomal RNA with Ribo-Zero rRNA removal Kit Bacteria (Illumina). Library prepared with TruSeq Stranded Total RNA Sample Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads filtering using fastp; fastpv 0.20.1
Aligment and differential expression analysis with Rockhopper; Rockhopper v2.03
Genome_build: Shewanella baltica OS185 NC_009665.1
Supplementary_files_format_and_content: Wig files generated by Rockhopper software. Scores represent normalized counts.
Supplementary_files_format_and_content: Rockhopper results table containing raw counts, normalized counts, fold change calculations and p values.
|
| |
|
| Submission date |
May 20, 2020 |
| Last update date |
May 21, 2020 |
| Contact name |
Pawel Olszewski |
| E-mail(s) |
[email protected]
|
| Organization name |
Medical University of Gdansk
|
| Department |
3P Medicine Laboratory
|
| Street address |
Debinki 7
|
| City |
Gdansk |
| ZIP/Postal code |
80-211 |
| Country |
Poland |
| |
|
| Platform ID |
GPL28560 |
| Series (1) |
| GSE150927 |
Changes in Shewanella baltica transcriptome upon cold stress |
|
| Relations |
| BioSample |
SAMN14981430 |
| SRA |
SRX8368949 |
