{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Etienne Kornobis"],"organism":["Bacteroides thetaiotaomicron"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14274"],"description":["RNA originating from genetically modified B. thetaiotaomicron jmh43 containing the dead cas9 (dcas9) silencing construct targeting either the RepCHP gene of the Hankyphage prophage or a non-targeting guide (control). For each construct, there are three biological replicates. RNA was extracted at different time-points post induction with IPTG (dcas9 inducer), either 0, 1, 2, 6 or 22 h."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequencing was performed as a paired reads run for 50 bp sequences on a NextSeq2000","Growth Protocol - Bacteroides strains were grown in brain-heart infusion medium supplemented (BHIS) with cysteine 0.1%, hemin 5 μg/mL and sodium bicarbonate 0.2% (NaCOH3). Cultures were incubated statically at 37°C in a C400M Ruskinn anaerobic chamber (95% N2, 5%CO2) or in anaerobic bags (GenBag anaero, Biomerieux). E. coli strains were grown in Luria-Bertani (LB) broth (Corning) supplemented with or without ampicilin 100 μg/mL and incubated at 37°C aerobically with 180 rpm shaking.","Sample Collection - Overnight cultures were mixed with RNAprotect (Qiagen) in the anaerobic chamber to prevent RNA degradation and bacteria were lysed using QIAGEN Proteinase K and TE buffer containing lysozyme.","Nucleic Acid Extraction - Total RNA was extracted using the Direct Zol kit (Zymo Cat. R2050) according to the manufacturer’s instructions and treated with Dnase I from the same kit. RNA concentration, quality, and integrity from 3 independent replicates were checked using the 4195 Tapestation system (Agilent).","Library Construction - Ribosomal RNA depletion was performed using the Bacteria RiboZero Plus kit (Illumina). From rRNA-depleted RNA, directional libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit following the manufacturer’s instructions (Illumina). Libraries were checked for quality on Bioanalyzer DNA 1000 chips (Agilent). Quantification was performed with the fluorescent-based quantitation Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Count matrix provided are raw counts generated by FeatureCounts 2.0.1 with strand specificity."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of total RNA"],"species":["Bacteroides thetaiotaomicron"],"pubmed_authors":["Sol Vendrell Fernandez","Etienne Kornobis"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq data from Bacteroides thetaiotaomicron genetically modified to silence a prophage gene (RepCHP)","description":"RNA originating from genetically modified B. thetaiotaomicron jmh43 containing the dead cas9 (dcas9) silencing construct targeting either the RepCHP gene of the Hankyphage prophage or a non-targeting guide (control). For each construct, there are three biological replicates. RNA was extracted at different time-points post induction with IPTG (dcas9 inducer), either 0, 1, 2, 6 or 22 h.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2025-12-31T02:02:12.718Z","creation":"2024-07-22T14:40:09.174Z"},"accession":"E-MTAB-14274","cross_references":{"ENA":["ERP162202"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0004184"]}}