{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["li gang"],"instrument_platform":["Illumina HiSeq X"],"study_type":["RNA-seq of coding RNA"],"organism":["Streptococcus suis"],"species":["Streptococcus suis"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15431"],"description":["Streptococcus suis is one of the most important bacterial pathogens of pigs, it is also an important zoonotic pathogen. It can withstand environmental stress and respond rapidly to stress. However, the regulatory mechanisms involved in this process are not fully elucidated. MnmE is a multi-domain GTPase that is highly conserved in bacteria and eukaryotes, driving tRNA modification during translation. In this study, we constructed an mnmE deletion strain (ΔmnmE) and a complementary strain (CΔmnmE) using the wild-type strain 05ZYH33 of S. suis, and systematically studied the characteristics and functions of MnmE in S. suis through phenotypic and multi-omics analyses. Phenotypic analysis showed that the mnmE strain exhibited growth defects, reduced virulence, decreased environmental tolerance, reduced capacity for metal ion transport, and changes in protein synthesis capabilities. Multi-omics results indicated that cellular processes related to carbohydrate metabolism, transcription and translation, and inorganic ion transport and metabolism were affected, which corroborated the phenotypic analysis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - The RNeasy kit (Qiagen) and Ribo-Zero™ rRNA Removal Kit (EPICENTRE Biotechnologies) was used to isolate RNA and remove rRNA.","Sequencing - The library could be sequenced using Illumina HiSeqTM X TEN or other sequencer when necessary.","Sample Collection - The cells were collected at 4°C, and washed twice with precooled PBS buffer, and the pellets were frozen in liquid nitrogen.","Growth Protocol - All bacteria were cultured at 37°C. 5%CO2","Library Construction - A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads for eucaryote ( For prokaryote, rRNA was removed from total RNA using Ribo-Zero rRNA Removal Kit to purify mRNA). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. First strand cDNA was synthesized using random hexamer primer and RNaseH. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified and resolved with EB buffer, then terminal repair、A-tailing and adapter added were implemented. After size selecting and retrieving by AMPure XP beads, the products were used as the index PCR templates. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlus™ Real-Time PCR System(Thermo Fisher Scientific，MA，USA)(Library valid concentration＞10 nM)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["li gang","Huang Yuxuan"],"additional_accession":[]},"is_claimable":false,"name":"Comparison of RNA-seq of Streptococcus suis wild-type and ΔmnmE mutant strains","description":"Streptococcus suis is one of the most important bacterial pathogens of pigs, it is also an important zoonotic pathogen. It can withstand environmental stress and respond rapidly to stress. However, the regulatory mechanisms involved in this process are not fully elucidated. MnmE is a multi-domain GTPase that is highly conserved in bacteria and eukaryotes, driving tRNA modification during translation. In this study, we constructed an mnmE deletion strain (ΔmnmE) and a complementary strain (CΔmnmE) using the wild-type strain 05ZYH33 of S. suis, and systematically studied the characteristics and functions of MnmE in S. suis through phenotypic and multi-omics analyses. Phenotypic analysis showed that the mnmE strain exhibited growth defects, reduced virulence, decreased environmental tolerance, reduced capacity for metal ion transport, and changes in protein synthesis capabilities. Multi-omics results indicated that cellular processes related to carbohydrate metabolism, transcription and translation, and inorganic ion transport and metabolism were affected, which corroborated the phenotypic analysis.","dates":{"release":"2025-08-11T00:00:00Z","modification":"2025-08-01T11:26:20.266Z","creation":"2025-08-01T11:26:20.266Z"},"accession":"E-MTAB-15431","cross_references":{"ENA":["ERP177696"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184"]}}