{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["amaranta kahn"],"organism":["Synechocystis salina"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16709"],"description":["Mid-exponential Synechocystis Salina LEGE 06099 (OD ~0.5) cultures were split into four conditions in biological triplicate (n = 3) and supplemented with C12 dodecanoic acid (in DMSO) or DMSO alone (control); samples were collected at 30 min and 6 h for RNA-seq."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - RNA-Seq library preparation was performed by Novogene. Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.","Sample Collection - Mid-exponential cultures (OD ~0.5) were supplemented with 0.5 mM C12 dodecanoic acid (or DMSO as a control) and harvested after 30 min and 6 hours. 100 mL of culture from each flask was centrifuged at 3000 ×g for 10 minutes at 4 °C. Pellets were resuspended in 1mL RNAlater Stabilization buffer (Thermo Fisher Scientific) and incubated at room temperature for 5 min followed by 3,000g 5 min centrifugation. Pellets were stored at −80 °C until further analysis.","Nucleic Acid Extraction - Pellets were flash-frozen in liquid nitrogen and disrupted using a mortar and pestle. RNA extraction was carried out using the PureLink TM RNA Mini Kit  (Thermo Fisher Scientific) accordingto the manufacturer's protocol. DNA was removed using RapidOut DNA Removal Kit (Thermo Fisher Scientific);","Sequencing - Illumina sequencing (150 bp paired-end) was performed by Novogene. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - RNA-Seq raw data were quality-checked using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). Raw reads were quality trimmed using the BBDuk tool from BBMap. Quality trimming was performed on both left and right sides (qtrim=rl) and based on Phred quality score at Q20 (trimq=20). The remaining trimmed reads were aligned to the LEGE 06099 genome with Bowtie2 (Wickham, 2016). Read counts for each gene were obtained from the alignment files and GFF annotations by using FeatureCounts (Liao et al., 2013).The resulting count table was imported into R (v. 4.1.2) and analysed with DESeq2 (v. 3.14) (Love et al., 2014),"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Synechocystis salina"],"pubmed_authors":["amaranta kahn"],"additional_accession":[]},"is_claimable":false,"name":"Effect of dodecanoic acid (C12) on the expression of Synechocystis Salina LEGE 06099 genes by RNAseq transcriptomics analysis, 30 min and 6 h post supplementation.","description":"Mid-exponential Synechocystis Salina LEGE 06099 (OD ~0.5) cultures were split into four conditions in biological triplicate (n = 3) and supplemented with C12 dodecanoic acid (in DMSO) or DMSO alone (control); samples were collected at 30 min and 6 h for RNA-seq.","dates":{"release":"2026-03-23T00:00:00Z","modification":"2026-03-23T02:02:49.181Z","creation":"2026-03-03T10:00:32.251Z"},"accession":"E-MTAB-16709","cross_references":{"ENA":["ERP189817"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}