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Sample GSM8158834 Query DataSets for GSM8158834
Status Public on Mar 28, 2024
Title Control, biological replicate 1
Sample type SRA
 
Source name bacterial cell
Organism Escherichia coli O157:H7
Characteristics strain: TUV93-0
cell type: bacterial cell
treatment: Control
Growth protocol Cells were grown in MEM-HEPES and supplemented with or without 1mg/ml L-arabinose.
Extracted molecule total RNA
Extraction protocol RNA from samples was prepared using a Monarch Total RNA Miniprep kit (New England Biolabs) following the manufacturer’s instruction and treated with TURBO DNAse. Concentrations and quality were assessed using Qubit (ThermoFisher Scientific).
Ribosomal depletion and library assembly of DNA-free total RNA samples was carried out using an Illumina Ribo-Zero Tru-seq kit according to the manufacturer’s specifications.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing To estimate transcript abundance, SALMON was used under the default parameters for the mapping of reads to the E. coli O157:H7 strain EDL933 reference sequence (Accession GCA_000006665), retrieved from Ensembl. Transcript level counts outputted from SALMON were then summarised at the gene-level using tximport
Assembly: ASM666v1
Supplementary files format and content: txt files with transcript level counts
 
Submission date Mar 21, 2024
Last update date Mar 28, 2024
Contact name Curtis Cottam
E-mail(s) curtis.cottam@ncl.ac.uk
Organization name Newcastle University
Department Biosciences Institute
Street address The Medical School, Newcastle University, Framlington Place
City Newcastle upon Tyne
ZIP/Postal code NE2 4HH
Country United Kingdom
 
Platform ID GPL34321
Series (1)
GSE262155 Metabolism of L-arabinose converges with virulence regulation to promote enteric pathogen fitness
Relations
BioSample SAMN40568863
SRA SRX24016414

Supplementary file Size Download File type/resource
GSM8158834_CTRL_1.quant.txt.gz 62.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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