{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Wei Hong"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Clostridium difficile 630"],"species":["Clostridium difficile 630"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15575"],"description":["To reveal the effects of deleting the Δxtr gene in Clostridioides difficile, we first constructed a Δxtr knockout mutant and then examined the resulting phenotypic changes. Finally, to elucidate the underlying mechanisms, we performed RNA-sequencing-based transcriptome analysis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted from WT, Δxtr, and ::xtr using a bacterial total RNA extraction kit (DP430, TIANGEN, Beijing).","Library Construction - Once the samples were deemed satisfactory, the following steps were conducted for sequencing: (1) Removal of ribosomal RNA; (2) Enrichment and purification of mRNA; (3) Fragmentation of mRNA; (4) Construction of the sequencing library and quality assessment of the library.","Sample Collection - The WT, Δxtr, and ::xtr strains were inoculated into BHIS medium and cultured until the OD600 reached 0.6. The cultures were then centrifuged at at 13,500 × g for 10 minutes, the supernatant was removed, and the bacterial pellets of each strain were collected. The samples were transported with adequate dry ice in an foam box to Nanjing Personalomics Co., Ltd. for transcriptome sequencin","Sequencing - The sequencing library was then sequenced on the Illumina Novaseq 6000 platform."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Wei Hong"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of  Clostridioides difficile  Δxtr against wild-type strain control","description":"To reveal the effects of deleting the Δxtr gene in Clostridioides difficile, we first constructed a Δxtr knockout mutant and then examined the resulting phenotypic changes. Finally, to elucidate the underlying mechanisms, we performed RNA-sequencing-based transcriptome analysis.","dates":{"release":"2025-12-30T00:00:00Z","modification":"2025-12-30T02:02:11.887Z","creation":"2025-09-12T11:35:02.216Z"},"accession":"E-MTAB-15575","cross_references":{"ENA":["ERP180011"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}