Time course of the Arabidopsis root stem cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE131988 | GEO | 2019/10/15
REPOSITORIES: GEO
Similar Datasets
Project description:The goal of this dataset was to transcriptionally profile the roots of wox5-1 and seu-3 mutants. To accomplish this, we collected 1mm of tissue from the root tip of each mutant as well as Col-0 as a control. RNA was extracted from root tissue, libraries were prepared, and RNA-seq was performed. FPKM values were calulcated using Cufflinks.
2020-06-04 | GSE104945 | GEO
Project description:adt05-04_drn - drn/drn-l expressing cells vs non-expressing cells - DRN targets - In primordia timing (pt) mutant background DRN::erGFP transgenic cell culture (somatic embryos suitable to regenerate plants) has been protoplasted and protoplasts have been sorted for GFP+ and GFP- cells. Total RNA was extracted and sent to Evry for comparison (samples DRN a,b,c). DRN-L::erGFP transgenic cell culture has been protoplasted and protoplasts have been sorted for GFP+ and GFP- cells (samples DRN-L-2-1 and DRN-L-3-1). Keywords: null
2010-05-01 | GSE19799 | GEO
Project description:adt05-04_drn - drn/drn-l expressing cells vs non-expressing cells - DRN targets - In primordia timing (pt) mutant background DRN::erGFP transgenic cell culture (somatic embryos suitable to regenerate plants) has been protoplasted and protoplasts have been sorted for GFP+ and GFP- cells. Total RNA was extracted and sent to Evry for comparison (samples DRN a,b,c). DRN-L::erGFP transgenic cell culture has been protoplasted and protoplasts have been sorted for GFP+ and GFP- cells (samples DRN-L-2-1 and DRN-L-3-1). Keywords: null 5 dye-swap - CATMA arrays
2010-04-30 | E-GEOD-19799 | biostudies-arrayexpress
Project description:We isolated cells in the different developmental zones of the A. thaliana root at 3,4,5,6 and 7 days old (DO)
2017-09-18 | GSE97857 | GEO
Project description:Purpose: The root hair is a model for understanding evolution of individual cell differentiation programs in plants. We compare the expression of the genes that participate in root hair development between Arabidopsis and other vascular plants to assess the conservation/diversification of the root hair development programs in vascular plants. Methods: We used RNA-Seq, in triplicates, to measure the genome-wide transcription activity of the root-hair cells isolated by Fluorescence-activated cell sorting (FACS) in Arabidopsis (COBL9::GFP transgeneic line, AtRH) and rice (EXPA30::GFP transgenic line, OsRH). We also generated RNA-Seq data, in triplicates, on the Arabidopsis rhd6 WER::GFP and WT WER::GFP by FACS to identify the RHD6-regulating root hair morphogenesis genes (AtRHM). For Arabidopsis, rice, tomato, soybean, cucumber and maize, we used RNA-seq, in triplicates, to measure genome-wide transcription activity of root hair cells filtered by sieves after stirred in liquid nitrogen (HAIR genes). Each sample was trimmed to retain high-quality reads, mapped to the reference genome by TopHat, and quantified by Cufflinks. The number of raw reads of Arabidopsis rhd6 WER::GFP and WT WER::GFP sample was counted by HTSeq and analyzed by edgeR to identify the differentially expressed genes. Results: We defined the root-hair transcriptome in diverse vascular plant species and analyzed the relative conservation/divergence in the expression of a large set of gene families.
2017-05-11 | GSE85516 | GEO
Project description:Time course of the Arabidopsis root stem cells
| PRJNA545515 | ENA
Project description:Dexamethasone applied to WT, GR-AS2, GR-KAN1, GR-REV and GR-STM seedlings and expression measured at 0, 30, 60 and 120 minutes after Dex application. SRA Series SRP051213 BioProject PRJNA258547. All reps are bio reps. Expression values are geometric normalized FPKM values from Tophat/Cufflinks reads and mappings.
2016-07-01 | E-GEOD-70796 | biostudies-arrayexpress
Project description:Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to -Fe media for 24 hours. Little is known about how developmental cues affect the way cells interpret their environment. Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes. We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects. By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type. Experiment Overall Design: To gain a genome-scale understanding of the role that developmental processes play in regulating stimulus response, we examined the effect of -Fe stress on gene expression along the radial axis of the root. Cell identity is the main variable that changes along the radial axis with the epidermis representing the outermost tissue layer and the stele representing the inner most layer. 5 different GFP reporter lines were used to isolate specific populations of cells from the Arabidopsis root using FACS sorting of protoplasted cells. GFP-reporter lines were exposed to iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no ferrous sulfate) for 24 hours before hand.
2008-06-11 | E-GEOD-10501 | biostudies-arrayexpress
Project description:Purpose: Treatment of neuroblastoma cell liner BE(2)N is known to convert these cells from adrenergic morphology to one that resembles mesenchymal cells. The goal of this study is to characterize the transcriptomes of BE(2)N during the conversion process and determine if the transcription changes are consistent with previously defined ADRN and MES signature genes. Methods: BE2N cells were treated with DMSO for 26 days or with 10µM BrdU for 5, 11, 20 and 26 days. Total RNA was isolated with the RNeasy Mini kit (Qiagen), and the quality of the preparations assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). TruSeq stranded mRNA libraries were prepared and sequenced with paired-end 50 bps on Illumina NovaSeq 6000 by the WCM Genomics Core Facility. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing. RNA reads were aligned and mapped to theGRCh37 human reference genome by STAR (Version2.5.2) (https://github.com/alexdobin/STAR), and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM). The fold changes were calculated by directly comparing the FPKM values of samples and controls. Results: The gene expression changes in BrdU-treated BE2N cells were identified through comparison with DMSO-treated control cells. The list of up-regulated and down-regulated genes were found to overlap strongly with previously defined MES and ADRN signature genes, supporting the notion that BrdU triggers the transcriptional re-programming of ADRN cells into MES cells. Conclusion: This study indicates that the morphologic conversion mediated by BrdU treatment of neuroblastoma cells is accompanied by genome wide transcriptional re-programming.
2021-11-24 | GSE171379 | GEO
Project description:We analyze the globel gene expression changes in the tumor initiating cells of regressing miR-125b addicted tumors after oncomiR withdrawal For Histone-H2BGFP expression in DTG tumor cells, the U6 promoter was deleted in the PLKO-PGK-H2B-GFP vector throughNdeI-AgeI digestion, Quick Blunting Kit treatment (NEB), and self-ligation. The resulting PLNA-PGK-H2BGFP plasmid was packaged into lentivirus and used to infect ~1x106freshly sorted α6hiβ1hi DTG tumor cells. After 30 min, cells were then extensively washed and immediately engrafted onto backskins of Nude mice by intradermal transplantation. GFP+α6hiβ1hicells were FACS-isolated from resulting tumors and then serially transplanted as above. For RNA seq analysis of the miR-125b addicted tumor regression process, H2BGFP labeled DTG tumor cells were intradermally engrafted onto backskins of Nude mice (1x104cells/site). Tumors were allowed to grow to ~1cm diameter. Mice were then taken Off Dox by transferring them to regular food for 0, 4, 7 days. GFP+α6hiβ1hiwere then FACS-isolated from the tumors. Two or three independent replicates were collected for each time point. Total RNAswere extracted from the FACS-sorted cells using the miRNeasy Mini Kit (Qiagen) according to the vender’s protocol. Expression of miR-125b in each sample was quantified by RT-PCR using TaqMan MicroRNA Assays (Applied Biosystems). For RNA seq, RNA samples were submitted to the Genomics Resources Core Facility of the Weill Cornell Medical College for library construction using IlluminaTruSeq Stranded mRNA Sample Prep Kit and then sequencing using Illumina HiSeq2000. Resultswere analyzed via the Galaxy web platform using TopHat for initiate mapping and Cufflinks for transcripts assembling and expression level estimation (Computing FPKM: fragments per kilobase of exon per million fragments mapped). The MM9 genome assembly (UCSC Genome Browser) was used as reference genome for all analyses. Low expression genes
2014-02-12 | E-GEOD-54704 | biostudies-arrayexpress