{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE329nnn/GSE329458/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Escherichia coli Nissle 1917"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE329458"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Strand-specific RNA-seq of Escherichia coli Nissle 1917 delta_cra, delta_crp, and delta_cra_delta_crp knockout mutants","description":"This study used prokaryotic strand-specific RNA sequencing to characterize transcriptomic changes associated with knockout of two global transcriptional regulator genes, cra and crp, encoding catabolite repressor/activator (CRA) and cAMP receptor protein (CRP), respectively, in Escherichia coli Nissle 1917. Four genotypes were profiled: wild-type strain, delta_cra mutant, delta_crp mutant, and delta_cra_delta_crp double-knockout mutant. Cells were cultured in MS medium and harvested at OD600 = 0.6. Ribosomal RNA was depleted, strand-specific RNA-seq libraries were constructed, and paired-end sequencing reads were generated on an Illumina NovaSeq 6000 platform. Gene-level read count, RPKM, and TPM matrices were generated to compare expression profiles among genotypes.","dates":{"publication":"2026/09/02"},"accession":"GSE329458","cross_references":{"GSM":["GSM9704512","GSM9704511","GSM9704510","GSM9704520","GSM9704516","GSM9704515","GSM9704514","GSM9704513","GSM9704509","GSM9704519","GSM9704518","GSM9704517"],"GPL":["32576"],"GSE":["329458"],"taxon":["Escherichia coli Nissle 1917"],"PMID":["[42252666]"]}}