{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Rudy Antoine"],"organism":["Bordetella pertussis"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16727"],"description":["This experiment was designed to compare the transcriptome of a KO mutant of Bordetella pertussis (inactivation of bp2921,that we have called crpH) with that of the wt strain, BPSM. Because we observed that growth of the mutant was affected in low-aeration conditions, we grew wt and mutant bacteria with or without agitation (200 rpm) in SS medium supplemented with 20 mM MgSO4 (the latter was added to maximize expression of the operon containing the gene of interest)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted using Tri-Reagent, followed by two consecutive DNase I treatments, each followed by purification using AMPure XP beads to remove genomic DNA and contaminating solvents.","Sample Collection - Bacterial suspensions (8 ml) were collected at mid-exponential phase and centrifuged at 4,000 rpm for 15 minutes at 4°C after adding 2 mL of a phenol:ethanol solution (5:95, v/v).","Sequencing - Libraries were sequenced on an Illumina NextSeq 500 system (Illumina, Inc.) in high-output mode.","Library Construction - Strand-specific RNA-seq libraries were prepared with the QIAseq Stranded RNA Library Kit according to the manufacturer's instructions.","Growth Protocol - The bacteria were grown with or without agitation in SS medium supplemented with 20 mM MgSO4."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw RNA-seq reads were processed with Illumina quality control tools using default settings. Sequences shorter than 50 bp and/or that contained any ‘Ns’ and/or with a mean quality score lower than 30 were removed using PRINSEQ (http://prinseq.sourceforge.net/index.html). Next, rRNA-specific reads were filtered out by mapping all the reads on M. tuberculosis rRNA sequences using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Analysis of the RNA sequencing data was conducted using the SPARTA open-source software package with default parameters (https://sparta.readthedocs.io/en/latest/)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"species":["Bordetella pertussis"],"pubmed_title":["CrpH of Bordetella pertussis, a prototypic PepSY_TM protein  supporting heme-copper oxidoreductase function"],"pubmed_authors":["Françoise Jacob-Dubuisson","Majda Hachmi, Gauthier Roy*, Anne-Sophie Debrie, Stéphanie Slupek,  Rudy Antoine, Françoise Jacob-Dubuisson","Rudy Antoine"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of Bordetella pertussis WT BPSM and crpH knockout strains cultivated in high and low aeration","description":"This experiment was designed to compare the transcriptome of a KO mutant of Bordetella pertussis (inactivation of bp2921,that we have called crpH) with that of the wt strain, BPSM. Because we observed that growth of the mutant was affected in low-aeration conditions, we grew wt and mutant bacteria with or without agitation (200 rpm) in SS medium supplemented with 20 mM MgSO4 (the latter was added to maximize expression of the operon containing the gene of interest).","dates":{"release":"2026-03-31T00:00:00Z","modification":"2026-03-31T01:03:46.762Z","creation":"2026-03-05T13:06:56.614Z"},"accession":"E-MTAB-16727","cross_references":{"ENA":["ERP189951"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}