|
| Status |
Public on Nov 02, 2022 |
| Title |
Intra-amoebael C. jejuni-1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria + Amoeba
|
| Organisms |
Campylobacter jejuni; Acanthamoeba castellanii |
| Characteristics |
cell type: Bacteria + Amoeba
c.jejuni strain: 11168H
c.jejuni genotype: WT
a.castellanii genotype: T4
treatment: Intra-amoebal bacteria (25C)
time: 4 hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Triazole, quality was checked by agarose gel, library was prepared according to Illumina protocol and was sent for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Acastellanii-C-jejuni-1
|
| Data processing |
The paired-end reads were trimmed and filtered using Sickle v1.200. Bowtie2 was used to map the reads against the reference sequence: C. jejuni strains 11168H assembly GCA_900117385.1. Cufflinks suite was used to convert annotations from GFF to GTF format and Bedtools was used to generate transcript counts per samples. Statistical analysis was performed in R using the combined data generated from the bioinformatics as well as meta data associated with the study (multifactorial design). Adjusted p-value significance cut-off of 0.001 and log fold change cut-off of >1.5 was used for multiple comparison.
Assembly: GCF_000009085.1 (ASM908v1)
Supplementary files format and content: *_EDGE.out.rpkm_0.txt: Tab-delimited text files include #reads and RPKM.
|
| |
|
| Submission date |
Jun 24, 2022 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Fauzy Nasher |
| E-mail(s) |
[email protected]
|
| Organization name |
London School of Hygiene and Tropical Medicine
|
| Street address |
Keppel Street,
|
| City |
LONDON |
| ZIP/Postal code |
WC1E 7HT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL32395 |
| Series (1) |
| GSE206909 |
Campylobacter jejuni interactions with Acanthamoeba castellanii |
|
| Relations |
| BioSample |
SAMN29335028 |
| SRA |
SRX15890790 |
