{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Irene Oliván Muro"],"organism":["Nostoc sp. PCC 7120 = FACHB-418"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15589"],"description":["Bacterial biofilms are microbial communities that grow attached to a surface, embedded in a complex matrix composed of extracellular polymeric compounds such as exopolysaccharides. They are commonly induced in response to stresses such as desiccation or depredation, and display increased resilience. Model cyanobacterium Anabaena sp. PCC7120, typically cultured planktonically, is able to form biofilms. In order to advance in the understanding of phototrophic biofilm formation, we carried out comparative transcriptomic analysis of biofilm and planktonic Anabaena and observed vast alterations. A total of 1099 differentially expressed genes (DEGs) were identified, of which 641 could be assigned a functional annotation. Major central metabolic pathways were affected, including carbohydrate metabolism, photosynthesis, ribosome biogenesis andtranslation. nitrogen metabolism and cellular envelops maintenance, among others."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - NGS sequencing project started with quality control of the total RNA, where the RNA integrity number (RIN) and concentration are analysed to ensure it is of sufficient integrity and quantity. Library construction was performed by STAB VIDA Lda (Lisbon, Portugal), employing a Ribosomal Depletion Library Preparation Kit for library construction.","Nucleic Acid Extraction - Frozen pellets were suspended in 300 µl of a buffer containing 0.3 M sucrose and 10 mM sodium acetate at pH 4.5, to which 100 µl of 250 mM Na2-EDTA (pH 8.0), 400 µl lysis buffer (2% SDS, 10 mM sodium acetate, pH 4.5) and 1 ml of acid phenol at 65 °C were added. Samples underwent three cycles of 30 second vortexing and 2.5 min incubation at 65ºC before centrifugation at 12000 x g for 5 min. The aqueous phase was collected and RNA extracted with Trizol, Trizol-Chloroform and Chloroform, thoroughly mixing with each step. The final aqueous phase was mixed with 2 volumes of chilled absolute ethanol and precipitated O/N at -80ºC. After 30 min of centrifugation at 12000 x g, pellets were washed with chilled 70% ethanol, resuspended in nuclease-free water (Ambion) and treated with RNAse-free DNAse I (Roche). DNA elimination was ensured by Real time RT-PCR using housekeeping gene rnpB (Vioque et al., 1992). RNA was quantified spectrophotometrically using a SPECORD® PLUS Analytik Jena spectrophotometer.","Sequencing - RNAseq was performed by STAB VIDA Lda (Lisbon, Portugal) employinh the lllumina Novaseq platform for DNA library sequencing, using 150 bp paired-end sequencing reads. Samples produced 22,561,164-29,581,586 sequence reads.","Sample Collection - Anabaena sp. PCC7120 was grown in bespoke bubbling flasks from 0.25 OD750nm in 350 mL of fresh BG11, under 15 µmol photons m-2 s-2 -for 72 hours. Sessile (biofilm) and planktonic fractions were collected separately and their supernatants removed by centrifugation. Pooled cultures of either type were distributed into 80-100 mg wet mass samples. Cell pellets were resuspended in 600 µl of 50 mM Tris-HCl pH 8, 100 mM EDTA and 130 µl of chloroform and mixed thoroughly by inversion. The suspension was centrifuged at 12000 x g for 5 min, supernatants were removed and obtained pellets were flash frozen in liquid nitrogen for storage at -80ªC."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - RNAseq raw sequence data was analysed by STAB VIDA Lda using CLC Genomics Workbench 12.0.3. Firstly, raw sequences were trimmed into high quality data based on a threshold of ambiguity (two nucleotides), quality (0.01 probability error) and length (30 nucleotides minimum). These high quality reads were mapped against the Nostoc sp. PCC 7120 = FACHB-418 (GCA_000009705.1) reference genome with a length and similarity fraction value of 0.8.","Data Transformation - The result of mapping served to determine the gene expression levels based on the TPM (Trancripts per Million). Fold changes were calculated from the Generalized Linear Model GLM, which corrects for differences in library size between the samples and the effects of confounding factors. Differentially expressed genes (DEGs) were filtered through a false discovery rate (FDR) corrected p-value ≤0.05 and a fold change (≥2 or ≤−2) threshold."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Nostoc sp. PCC 7120 = FACHB-418"],"pubmed_authors":["Emma Sevilla Miguel","María Fillat Castejón","Irene Oliván Muro"],"additional_accession":[]},"is_claimable":false,"name":"Comparative transcriptomics of Anabaena sp. PCC7120 grown as biofilm under bubbling or their concurrent planktonic fractions","description":"Bacterial biofilms are microbial communities that grow attached to a surface, embedded in a complex matrix composed of extracellular polymeric compounds such as exopolysaccharides. They are commonly induced in response to stresses such as desiccation or depredation, and display increased resilience. Model cyanobacterium Anabaena sp. PCC7120, typically cultured planktonically, is able to form biofilms. In order to advance in the understanding of phototrophic biofilm formation, we carried out comparative transcriptomic analysis of biofilm and planktonic Anabaena and observed vast alterations. A total of 1099 differentially expressed genes (DEGs) were identified, of which 641 could be assigned a functional annotation. Major central metabolic pathways were affected, including carbohydrate metabolism, photosynthesis, ribosome biogenesis andtranslation. nitrogen metabolism and cellular envelops maintenance, among others.","dates":{"release":"2026-05-08T00:00:00Z","modification":"2026-05-08T07:47:45.461Z","creation":"2025-09-12T13:53:13.008Z"},"accession":"E-MTAB-15589","cross_references":{"ENA":["ERP180026"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}