{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Munissa Sadykova"],"organism":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16110"],"description":["Plants have developed various mechanisms of stress response, including stress memory. Epigenetic mechanisms play a vital role in plants' stress memory. In this experiment, DNA methylation dynamics in primed and non-primed A. thaliana plants was evaluated under cold stress to understand the role of epigenetic mechanisms in cold stress responses and memory."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Plants were grown in 0.5x Murashige and Skoog (MS) media with 0.8% agar with 0.1% sucrose content at 22°C with a long day (16 h light / 8 h dark) for 9 days, then transferred to soil for stress treatment and until the sample collection.","Nucleic Acid Extraction - Genomic DNA (gDNA) was extracted from 0.1g of frozen plant leaf tissue using the Nucleon PhytoPure DNA extraction kit (Cytiva, USA) according to the protocol manual from the manufacturer.","Sequencing - Paired-end sequencing with NovaSeq 6000 (Illumina).","Library Construction - EM-seq libraries were constructed using NEBNext Enzymatic Methyl-seq (EM-seq™) kit for Illumina (New England BioLabs, USA) and NEBNext® Multiplex Oligos for Enzymatic Methyl-seq (Unique Dual Index Primer Pairs) (New England BioLabs, USA) following the manufacturer’s recommendations.","Sample Collection - RNA-seq was performed for 25-days-old Arabidopsis thaliana plants grown in control conditions (22°C) (non-primed, C), plants primed with cold stress at 4°C for 3 days (Priming only, P), plants triggered with cold stress at 4°C for 3 days (Triggering only, T), and the primed and triggered plants (Priming and Triggering, PT). Leaf samples of the plants were collected."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Results were analyzed with nf-core pipeline “methylseq” (revision 2.5.0) with --comprehensive true --em_seq true --cytosine_report true parameters. Read quality control and trimming were performed with FastQC (v. 0.11.9) and Trim Galore! (v. 0.6.7), respectively. BAM files from replicates were merged and reads were then aligned to the TAIR10 genome. Methylation calls were extracted using the Bismark (v. 0.24.0) software. Alignment quality was assessed with Qualimap (v. 2.2.2-dev). Following the read processing with the nf-core pipeline, cytosine reports (CX_report) were manually generated using the bismark_methylation_extractor function of Bismark (v. 0.23.0) with options --CX --cytosine_report."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["methylation profiling by high throughput sequencing"],"species":["Arabidopsis thaliana"],"pubmed_authors":["Munissa Sadykova"],"additional_accession":[]},"is_claimable":false,"name":"Enzymatic Methyl sequencing (EM-seq) of primed and non-primed Arabidopsis thaliana under cold-stress","description":"Plants have developed various mechanisms of stress response, including stress memory. Epigenetic mechanisms play a vital role in plants' stress memory. In this experiment, DNA methylation dynamics in primed and non-primed A. thaliana plants was evaluated under cold stress to understand the role of epigenetic mechanisms in cold stress responses and memory.","dates":{"release":"2026-03-13T00:00:00Z","modification":"2026-03-13T02:02:31.432Z","creation":"2025-11-13T21:33:52.115Z"},"accession":"E-MTAB-16110","cross_references":{"ENA":["ERP184403"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002761","EFO_0005518","EFO_0003816","EFO_0004184"]}}