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| Status |
Public on Nov 02, 2022 |
| Title |
Control-1 |
| Sample type |
SRA |
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| Source name |
Bacteria
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| Organism |
Campylobacter jejuni |
| Characteristics |
cell type: Bacteria
c.jejuni strain: 11168H
c.jejuni genotype: WT
treatment: Control (25C)
time: 4 hrs
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Cjejuni-1
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| 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.
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| Submission date |
Jun 24, 2022 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Fauzy Nasher |
| E-mail(s) |
[email protected]
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| Organization name |
London School of Hygiene and Tropical Medicine
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| Street address |
Keppel Street,
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| City |
LONDON |
| ZIP/Postal code |
WC1E 7HT |
| Country |
United Kingdom |
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| Platform ID |
GPL28665 |
| Series (1) |
| GSE206909 |
Campylobacter jejuni interactions with Acanthamoeba castellanii |
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| Relations |
| BioSample |
SAMN29335031 |
| SRA |
SRX15890787 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6266731_Cjejuni-1_EDGE.out.rpkm_0.txt.gz |
18.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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