{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jorge Guio"],"organism":["Nostoc sp. PCC 7120 = FACHB-418"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17710"],"description":["This study aims to identify the regulon of the calB (all2080) gene in the filamentous cyanobacterium Anabaena sp. PCC 7120. We performed differential expression analysis (RNA-seq) on a calB deletion mutant and the wild-type strain to characterize the physiological impact of the absence of this regulator"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Frozen pellets were resuspended in sucrose-sodium acetate buffer, lysis buffer (2% SDS), and acid phenol at 65°C. Following extraction with Trizol and Chloroform, RNA was precipitated overnight in absolute ethanol at -80°C. Samples were treated with RNase-free DNase I (Roche), and the absence of DNA was confirmed by Real-Time PCR. RNA was quantified spectrophotometrically.","Library Construction - 12 samples were processed for library preparation using an Illumina RNA kit. Quality control was performed by assessing RNA integrity with a Fragment Analyzer and concentration via Qubit assay","Sequencing - Sequencing was conducted on an Illumina NovaSeq platform with a 2x150 bp configuration. The project generated approximately 10M paired-end reads per sample","Sample Collection - Cells were harvested by centrifugation at 4000g for 5 min at 4°C, transferred to a 2 ml Eppendorf and collected by centrifugation at 16,500g for 5 min at 4°C. The supernatant was removed, and the cell pellet was resuspended in 600 μl of 50 mM Tris–HCl pH 8, 100 mM EDTA, and 130 μl of chloroform, then flash-frozen in liquid nitrogen and stored at -80°C."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - aw sequence reads are subjected to quality filtering and adapter trimming. Trimmed reads are mapped to the Anabaena sp. PCC 7120 reference genome. Gene expression levels are quantified and normalized (typically using DESeq2 median-of-ratios or similar TMM normalization) to account for differences in sequencing depth and RNA composition."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NA","Fragment Analyzer, Qubit assay","Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Nostoc sp. PCC 7120 = FACHB-418"],"pubmed_authors":["Jorge Guio"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic analysis of the Anabaena sp. PCC 7120 calB (all2080) deletion strain compared to wild-type under standard growth conditions","description":"This study aims to identify the regulon of the calB (all2080) gene in the filamentous cyanobacterium Anabaena sp. PCC 7120. We performed differential expression analysis (RNA-seq) on a calB deletion mutant and the wild-type strain to characterize the physiological impact of the absence of this regulator","dates":{"release":"2026-10-06T00:00:00Z","modification":"2026-10-06T00:38:12.214Z","creation":"2026-10-01T15:45:44.861Z"},"accession":"E-MTAB-17710","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}