|
| Status |
Public on Mar 07, 2018 |
| Title |
Wild-type in vivo, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Infected murine muscle tissue
|
| Organism |
Clostridium perfringens |
| Characteristics |
strain: JIR325
source: Infected murine muscle tissue
|
| Growth protocol |
In vitro cells were grown for 90 min trypticase peptone broth
In vivo cells were injected into murine muscles and the muscle tisses removed and extracted after 90 min
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was then isolated using TRIzol reagent. The RNA aliquot was treated with Turbo DNase (Ambion) at 37°C for 30-60 min to eliminate DNA contamination. Contaminating host RNA was depleted from the sample using a MICROBEnrichTM kit (Ambion) in accordance with the manufacturer’s instructions. A total of 5 μg of pooled RNA was subjected to repeated cycles of bacterial RNA enrichment to ensure the almost complete depletion of the host RNA. Next, bacterial ribosomal RNA (rRNA) was depleted from the preparation using a Ribo-Zero rRNA removal kit (Epicentre) as per the manufacturer’s instructions. Libraries for bacterial RNA-seq were then prepared using an Illumina TruSeq RNA sample preparation kit v2. RNA-seq analysis of the enriched RNA samples from the in vivo- and in vitro-derived cells was carried out on Illumina Hi-seq and Mi-seq instruments, respectively.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Analysis was performed using the Nesoni pipeline. (https://github.com/Victorian-Bioinformatics-Consortium/nesoni)
Reads were firsted clipped of low quality and adaptor sequence using the Nesoni "clip" tool.
Reads were aligned using SHRiMP 2.2.3.
Fragments (reads or read-pairs) aligning to genes were counted using the Nesoni "count" tool. Where a read aligned equally well to multiple genes, it was counted once toward all best-aligning genes. Reads were produced from multiple sequencing runs for the "in vivo" samples, these have been pooled together to produce a single count for each biological sample.
Genome_build: Clostridium perfringens strain 13, NCBI reference sequences NC_003366.1 and NC_003042.1
Supplementary_files_format_and_content: counts.csv - Fragment counts for each gene and sample in CSV format.
|
| |
|
| Submission date |
Mar 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Julian Rood |
| E-mail(s) |
julian.rood@monash.edu
|
| Organization name |
Monash University
|
| Department |
Microbiology
|
| Lab |
Functional Biology of Bacterial Pathogens
|
| Street address |
Wellington Rd
|
| City |
Clayton |
| State/province |
VIC |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL23210 |
| Series (1) |
| GSE96890 |
Comparative RNAseq analysis of C. perfringens strain JIR325 grown in vivo and in vitro. |
|
| Relations |
| BioSample |
SAMN06627062 |
| SRA |
SRX2661339 |
