|
| Status |
Public on Jul 01, 2014 |
| Title |
Campylobacter jejuni fur perR mutant RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organism |
Campylobacter jejuni |
| Characteristics |
strain: NCTC 11168
genotype/variation: fur::kan perR:cm
phase: late log growth
|
| Growth protocol |
The wildtype and fur perR mutant of Campylobacter jejuni strain NCTC 11168 were grown to late log phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified omitting size selection, to avoid the loss of small RNA molecules. The exclusion of rRNA and tRNA was also omitted, to avoid the potential loss of other RNA species. RNA was isolated using hot phenol (Mattatall & Sanderson, 1996), to ensure that small RNAs would not be removed by the extraction procedure. The RNA was treated with DNase I to remove residual genomic DNA.
The RNA samples were used to generate strand-inspecific RNA-seq libraries for Illumina sequencing, using instructions from the manufacturer (Illumina), and further analysed using an Illumina HiSeq2000 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
cDNA libraries constructed, using standard Illumina protocols. Libraries are not strand-specific
|
| Data processing |
Sequences were obtained from FASTQ files, processed by the software provided by the HiSeq2000 sequencing service at The Genome Analysis Centre, Norwich, UK
Transcript levels of individual genes were expressed as Reads Per Kilobase per Million mapped reads (RPKM) values, calculated after mapping of reads using CLC Genomics Workbench v5 (CLC Bio).
The reads were also aligned against the C. jejuni genome NCTC 11168 genome sequence using Segemehl version 0.0.9.3 (Hoffmann et al., 2009), and converted into number of reads per nucleotide position, for the plus and minus strand of the genome (*.gr files)
Graphs representing the number of mapped reads per nucleotide were loaded in the Integrated Genome Browser software from Affymetrix (Nicol et al., 2009).
Genome_build: Campylobacter jejuni NCTC11168: NC_002163.1
Supplementary_files_format_and_content: Histogram files for use in the Integrated Genome Browser software from Affymetrix (Nicol et al., 2009). Scores represent the number of reads per nucleotide position
Supplementary_files_format_and_content: CSV files containing gene designation, RPKM value and coordinates used for Chromosome region start and Chromosome region end
|
| |
|
| Submission date |
Aug 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Arnoud van Vliet |
| E-mail(s) |
arnoud.vanvliet@ifr.ac.uk
|
| Phone |
+44-1603-255250
|
| Organization name |
Institute of Food Research
|
| Department |
Gut Health and Food Safety Programme
|
| Street address |
Colney Lane
|
| City |
Norfolk |
| ZIP/Postal code |
NR4 7UA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17549 |
| Series (1) |
| GSE49687 |
RNA-sequencing of Campylobacter jejuni NCTC 11168 wildtype and fur perR mutant |
|
| Relations |
| BioSample |
SAMN00996390 |
| SRA |
SRX335107 |
