|
| Status |
Public on Mar 15, 2019 |
| Title |
YeO:3 (Y1) 25°C stationary growth phase, not enriched 1 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro culture
|
| Organism |
Yersinia enterocolitica |
| Characteristics |
strain: Y1
grwoth condition: 25C, exponential growth phase
|
| Treatment protocol |
Purification of mRNA was done using human/mouse/rat ScriptSeq complete kit (Illumina). Following the purification, the RNA was used for library preparation using Script Seq v2 Library preparation kit (Illumina).
|
| Growth protocol |
bacteria were grown in LB medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated using hot phenol extraction
cDNA libraries were constructed using NEBNext Multiple Small RNA Library Prep Set (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
not enriched for primary transcripts
|
| Data processing |
library quality assessment using FastQC
alignment vs. reference genome using Bowtie2 with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq) and subsequent RPKM normalization
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization
Genome_build: NC_008800.1 Yersinia enterocolitica subsp. enterocolitica 8081; CP030980/CP030981 Yersinia enterocolitica subsp. Y1
Supplementary_files_format_and_content: *.tab files: CSV format with raw read counts per gene; tar-Archive DESeq2_results.tar.gz with DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes
|
| |
|
| Submission date |
Sep 04, 2018 |
| Last update date |
Mar 15, 2019 |
| Contact name |
Michael Beckstette |
| Organization name |
Helmholtz Centre for Infection Research
|
| Department |
Molecular Infection Biology
|
| Lab |
Experimental Immunology
|
| Street address |
Inhoffenstrase 7
|
| City |
Braunschweig |
| State/province |
Lower Saxony |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19851 |
| Series (1) |
| GSE119404 |
Transcriptomic profiling of Yersinia enterocolitica O:3 and O:8 reveals serotype-specific expression differences leading to largely different YstA toxin levels |
|
| Relations |
| BioSample |
SAMN09950625 |
| SRA |
SRX4636454 |
