biostudies-arrayexpressImani MadisonArabidopsis thalianahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15703RNA-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.biostudies-arrayexpressSample Collection - FACS-sorted protocols were collected from 5d old roots that had been iron deficiency-starved for 24hLibrary Construction - Extracted RNA was converted to cDNA using the Takara SMARTer cDNA synthesis kitSample Treatment - Plants were transferred to iron deficiency media for 24h before sortingGrowth Protocol - Growth on MS for 4d then transferred to iron deficient media for 24hNucleic Acid Extraction - Sorted cells were immediately frozen on liquid nitrogen then RNA was extracted using the Qiagen RNeasy micro kitSequencing - Bulk-sorted pooled samples were sequenced by Illumina sequencingOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Expression values of the DEGs were normalized in edgeR (RPKM values)MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 4000RNA-seq of coding RNAArabidopsis thalianaIron deficiency changes regulatory mechanisms governing sieve element cell differentiationImani 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. LongImani MadisonfalseRNA-seq of Arabidopsis root sieve element markers at 24h of iron deficiencyRNA-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.2025-11-21T00:00:00Z2026-05-30T16:35:21.147Z2025-10-13T15:18:05.76ZE-MTAB-15703ERP182061EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969