{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Wendy Le Mouëllic"],"organism":["Mycobacterium tuberculosis H37Rv"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15580"],"description":["RNA-seq analysis of total RNA was conducted on wild-type and ΔsubI Mycobacterium tuberculosis (H37Rv strain) to uncover transcriptomic adaptations resulting from the deletion of subI, the gene encoding the sulfate-binding subunit of the SubI-CysTWA sulfate transporter."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - WT and ΔsubI H37Rv were grown in triplicates in 7H9 medium supplemented with 10% ADC, 0,05% Tyloxapol, 1mM MgSO4, and 1mM cysteine until OD600 =0.8.","Sequencing - The cDNA library was The cDNA library was paired end sequenced on an Illumina NovaSeqXPlus™ platform (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles).sequenced on an Illumina NovaSeqXPlus™ platform (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles).","Library Construction - Total Bulk RNA sequencing was performed Each extracted total RNA sample was barcoded with CEL-seq primers during the enzymatic lysis. It was then followed by fragmentation, end repair, poly(A)-tailing, reverse transcription, and second-strand synthesis. After second-strand synthesis, the barcoded samples were pooled into one library and amplified using in vitro transcription. Further, ribosomal aRNA was depleted. After depletion, adapter ligation, reverse transcription, and indexing PCR were performed to prepare a cDNA library.","Nucleic Acid Extraction - Total RNA was extracted from 10 mL of bacterial cultures grown to logarithmic phase (OD600nm = 0.8) using RNeasy kit (Qiagen)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Raw sequencing data was processed using Cutadapt (v4.9) to remove adapter sequences and homopolymers, followed by Ribodetector (v0.3.1) to filter out ribosomal reads. Processed reads were then aligned to the Mycobacterium tuberculosis H37Rv reference genome (assembly ASM19595v2) using STARsolo (v2.7.11b), with the parameter --soloFeatures set to GeneFull_Ex50pA.","Data Transformation - The processed file 'raw_counts_all_samples' contains the unnormalized raw read counts for all mapped genes across each sample."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of total RNA"],"species":["Mycobacterium tuberculosis H37Rv"],"pubmed_authors":["Wendy Le Mouëllic","Olivier Neyrolles"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of wild-type H37Rv and ΔsubI strains of Mycobacterium tuberculosis","description":"RNA-seq analysis of total RNA was conducted on wild-type and ΔsubI Mycobacterium tuberculosis (H37Rv strain) to uncover transcriptomic adaptations resulting from the deletion of subI, the gene encoding the sulfate-binding subunit of the SubI-CysTWA sulfate transporter.","dates":{"release":"2025-09-15T00:00:00Z","modification":"2026-06-16T14:20:33.304Z","creation":"2025-09-12T10:59:58.342Z"},"accession":"E-MTAB-15580","cross_references":{"ENA":["ERP180007"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}