{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Anna Wójcik"],"organism":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16183"],"description":["The pWOX2::H2B-GFP Arabidopsis line was used to induce somatic embryogenesis following the SE induction protocol described by Gaj (2001). After three days of somatic embryogenesis induction, nuclei were isolated from the upper part of the explants (immature zygotic embryos) and subjected to fluorescence-activated nuclear sorting (FANS). During sorting, two nuclear fractions were collected: GFP-positive and GFP-negative nuclei. RNA was extracted, converted to cDNA and sequenced on an illumina NovaSeq SP SR100."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - RNA was extracted from FANSed nuclei with Trizol LS (Ambion).","Sequencing - The prepared librieries were sequenced on a Illumina NovaSeq 200 platform","Sample Treatment - Somatic embryogenesis was induced by Gaj 2001 protocol with 4,5uM of 2,4-D in the medium.","Library Construction - cDNA was synthesized using SMARTER technology (clontech).","Sample Collection - The upper part of the explants after 3 days of somatic embryogenesis culture was taken for nuclei isolation.","Growth Protocol - Arabidopsis was grown on soil under a 16h-light/8h-dark regime at 21C"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Arabidopsis thaliana"],"pubmed_title":["FANS uncovers WOX2-associated early regulators of auxin-induced somatic embryogenesis in Arabidopsis"],"pubmed_authors":["Anna M. Wójcik, Weronika M. Buchcik; Viktoriia Verezunska, Ruben Gutzat, Ortrun Mittelsten Scheid and Małgorzata D. Gaj","Anna Wójcik"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq after FANS of WOX2 marked cells after 3 days of somatic embryogenesis induction in Arabidopsis.","description":"The pWOX2::H2B-GFP Arabidopsis line was used to induce somatic embryogenesis following the SE induction protocol described by Gaj (2001). After three days of somatic embryogenesis induction, nuclei were isolated from the upper part of the explants (immature zygotic embryos) and subjected to fluorescence-activated nuclear sorting (FANS). During sorting, two nuclear fractions were collected: GFP-positive and GFP-negative nuclei. RNA was extracted, converted to cDNA and sequenced on an illumina NovaSeq SP SR100.","dates":{"release":"2026-01-20T00:00:00Z","modification":"2026-01-20T15:16:25.591Z","creation":"2025-11-19T11:31:07.797Z"},"accession":"E-MTAB-16183","cross_references":{"ENA":["ERP185321"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184","EFO_0003969"]}}