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Sample GSM5292216 Query DataSets for GSM5292216
Status Public on Sep 30, 2021
Title ∆rrpA rep3
Sample type SRA
 
Source name not applicable
Organism Campylobacter jejuni
Characteristics strain: 11168H
genotype: rrpA mutant
culture method: cell suspension culture (6 hrs growth)
Growth protocol RNA-Seq was used to identify differentially expressed genes between wild type strains, ∆rrpA and ∆rrpB mutants at mid-log (~6 hrs) of growth. 11168H wild type, 11168H∆rrpA, 11168H∆rrpB and 11168H∆rrpAB were plated out on BA plates and incubated at 37°C under microaerobic conditions for 6 hrs. 11168H is hypermotile variant of strain 11168 which is the background strain for the samples used in the study.
Extracted molecule total RNA
Extraction protocol RNA was extracted from the pelleted bacteria cells using PureLink™ RNA Mini Kit (Invitrogen), following manufactures protocol. RNA was isolated from five independent experiments performed on different days Ribosomal RNA was depleted using Ribominus (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Description 11168H_rrpA_biological_3
Data processing Raw reads were obtained from an Illumina Miseq paired-end sequencing platform (Illumina).
The paired-end reads were trimmed and filtered using Sickle v1.200 by using a sliding window approach and trimming the reads where the average base quality drops below 20. Only the reads that were above 10 bp length were kept after trimming. Bowtie2 was used to map the reads against the reference sequences; C. jejuni strains 11168H assembly GCA_900117385.1. This generated the mapping in SAM format which were converted to BAM format using Samtools and were index sorted. We used gffread from cufflinks suite to convert annotations from GFF to GTF format. These were used in Bedtools (with multicov-bams option)with the mapped reads to generate transcript counts per samples. A shell utility by the authorswas then used to collate all these transcripts into a n=20 samples x p=1,628 transcripts for 11168H strain. 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). We used DESeq DataSet from Matrix()function fromDESeq2 package with the adjusted p-value significance cut-off of 0.05 and log fold change cut-off of 1.5. This function uses negative binomial GLM to obtain maximum likelihood estimates for the transcripts log fold change between the two conditions.
Genome_build: C. jejuni strains 11168H assembly GCA_900117385.1.
Supplementary_files_format_and_content: Excel file include RPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date May 12, 2021
Last update date Sep 30, 2021
Contact name Fauzy Nasher
E-mail(s) fauzy.nasher1@lshtm.ac.uk
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 GPL22824
Series (1)
GSE174333 MdaB and NfrA, two novel reductases important in the survival and persistence of the major enteropathogen Campylobacter jejuni
Relations
BioSample SAMN19117169
SRA SRX10856721

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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