{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Imani Madison"],"organism":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15703"],"description":["RNA-seq of pPEAR1::dBOX-YFP, pPEAR1-erGFP, and pC2-YFP to characterize the transcriptome associated with progressively more differentiated sieve elements. pPEAR1::dBOX-YFP is the proxy for early / phloem initials. pPEAR1-erGFP is the proxy for transit amplifying protophloem. pC2-YFP is the proxy for differentiation sieve elements. Each marker line was grown for 4 days in standard MS (Murashige & Skoog) media then transferred to iron deficient media (Murashige & Skoog containing ferrozine to chelate any iron present so that it's biounavailable). At 24h after transfer, roots were protoplasted and sorted using Fluorescence Activated Cell Sorting (FACS) to isolate GFP-positive or YFP-positive cells. Then, RNA-seq was performed in the sorted cell populations."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - FACS-sorted protocols were collected from 5d old roots that had been iron deficiency-starved for 24h","Library Construction - Extracted RNA was converted to cDNA using the  Takara SMARTer cDNA synthesis kit","Sample Treatment - Plants were transferred to iron deficiency media for 24h before sorting","Growth Protocol - Growth on MS for 4d then transferred to iron deficient media for 24h","Nucleic Acid Extraction - Sorted cells were immediately frozen on liquid nitrogen then RNA was extracted using the Qiagen RNeasy micro kit","Sequencing - Bulk-sorted pooled samples were sequenced by  Illumina sequencing"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Expression values of the DEGs were normalized in edgeR (RPKM values)"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of coding RNA"],"species":["Arabidopsis thaliana"],"pubmed_title":["Iron deficiency changes regulatory mechanisms governing sieve element cell differentiation"],"pubmed_authors":["Imani Madison, Eli D. Buckner, Maria Angels de Luis Balaguer, Jina Song, Dipali Srivastava, Devarshi Selote, Aitch Hunt, Eduardo Bueso, Rosangela Sozzani, Cranos Williams, Terri A. Long","Imani Madison"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of Arabidopsis root sieve element markers at 24h of iron deficiency","description":"RNA-seq of pPEAR1::dBOX-YFP, pPEAR1-erGFP, and pC2-YFP to characterize the transcriptome associated with progressively more differentiated sieve elements. pPEAR1::dBOX-YFP is the proxy for early / phloem initials. pPEAR1-erGFP is the proxy for transit amplifying protophloem. pC2-YFP is the proxy for differentiation sieve elements. Each marker line was grown for 4 days in standard MS (Murashige & Skoog) media then transferred to iron deficient media (Murashige & Skoog containing ferrozine to chelate any iron present so that it's biounavailable). At 24h after transfer, roots were protoplasted and sorted using Fluorescence Activated Cell Sorting (FACS) to isolate GFP-positive or YFP-positive cells. Then, RNA-seq was performed in the sorted cell populations.","dates":{"release":"2025-11-21T00:00:00Z","modification":"2026-05-30T16:35:21.147Z","creation":"2025-10-13T15:18:05.76Z"},"accession":"E-MTAB-15703","cross_references":{"ENA":["ERP182061"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}