|
| Status |
Public on Jul 07, 2018 |
| Title |
C. jejuni PT14 spiral stationary phase replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Spiral morphotype stationary phase
|
| Organism |
Campylobacter jejuni |
| Characteristics |
strain: PT14
growth phase: Stationary
cell morphology: Spiral
|
| Treatment protocol |
Short C. jejuni spiral cells were separated from filamentous cells using a 0.8 µm sterile nitrocellulose membrane on a vacuum manifold.
|
| Growth protocol |
Three independent biological replicates of C. jejuni PT14 were inoculated into 500 ml of sterile MEM (minimum essential medium without glutamine and phenol red; Catalogue number 51200-038; Life Technologies Ltd) with 10 mM sodium pyruvate, to a final density of approximately 10exp5 CFU/ml. The culture flasks were incubated in a shaking incubator at 100 rpm, at 37 °C under microaerobic conditions (approximately 7% O2, v/v) for 30 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the cell morphotypes using the Trizol Max Bacterial Isolation kit (Invitrogen) and purified using an RNeasy Mini kit (Qiagen) and the integrity was measured using a Bioanalyser 2100 (Agilent Technologies).
Ribosomal RNAs were depleted from the total RNAs using the Ribo-Zero™ Magnetic Kit for bacteria (Illumina) and used to prepare cDNA libraries using the NEBNext Ultra directional Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina CASAVA v1.8.2
Illumina bcl2fastq v1.8.4
CLC Genomics Workbench 10.1 Trim and Quality Filter
CLC Genomics Workbench 10.1 RNAseq strand specific abundance and normalisation recorded as TPM (Transcripts Per Kilobase Million) and RPKM (Reads Per Kilobase Million)
Genome_build: C. jejuni PT14 NCBI accession CP003871.2
Supplementary_files_format_and_content: tab-delimited text files that include TPM and RPKM values for each gene location
|
| |
|
| Submission date |
Jul 06, 2018 |
| Last update date |
Jul 08, 2018 |
| Contact name |
Ian Frank Connerton |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Nottingham
|
| Department |
School of Biosciences
|
| Lab |
Food Sciences
|
| Street address |
College Road, Sutton Bonington
|
| City |
Loughborough |
| State/province |
Leicestershire |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19974 |
| Series (1) |
| GSE116729 |
Defining stationary phase transcriptomes of Campylobacter jejuni cell morphotypes |
|
| Relations |
| BioSample |
SAMN09623300 |
| SRA |
SRX4348137 |
