High-throughput single cell transcriptome profiling of plant tissue
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE116614 | GEO | 2018/08/28
REPOSITORIES: GEO
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Project description:Single-cell transcriptome analysis of heterogeneous tissues can provide high-resolution windows into the spatiotemporal dynamics of developmental processes and environmental responses. Here we use the high-hroughput Drop-seq approach to profile the transcriptomes of over 12,000 individual cells from the Arabidopsis root. We identify marker genes for a diversity of cell types, capture cell-type frequency and gene expression alterations in response to sucrose, and illuminate the transcriptome changes that occur across endodermis development.
2019-05-13 | GSE122687 | GEO
Project description:Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. aChIP enables precise profiling of histone modifications in all tested EIPOs as well as transcription factors and chromatin-modifying enzymes. Notably, it significantly enhances ChIP efficiency and uncovers numerous novel modified sites compared to previous methods in vegetativetissues. Remarkably, aChIP unveils the first histone modification landscape of dry rapeseed seeds, illuminating the intricate roles of histone marks in EIPOs. Together, aChIP is a potent, efficient, and sensitive approach for comprehensive chromatin protein profiling across virtually all plant tissues, advancing plant epigenomics and functional genomics research, particularly within EIPOs.
2024-04-28 | GSE243805 | GEO
Project description:Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. aChIP enables precise profiling of histone modifications in all tested EIPOs as well as transcription factors and chromatin-modifying enzymes. Notably, it significantly enhances ChIP efficiency and uncovers numerous novel modified sites compared to previous methods in vegetativetissues. Remarkably, aChIP unveils the first histone modification landscape of dry rapeseed seeds, illuminating the intricate roles of histone marks in EIPOs. Together, aChIP is a potent, efficient, and sensitive approach for comprehensive chromatin protein profiling across virtually all plant tissues, advancing plant epigenomics and functional genomics research, particularly within EIPOs.
2024-04-28 | GSE243804 | GEO
Project description:A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and 166b. Endodermally produced miR165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage dependent manner.
2010-04-15 | GSE16469 | GEO
Project description:Exploiting CRISPR-Cas9 technology to investigate individual histone modifications
| PRJEB21645 | ENA
Project description:A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and 166b. Endodermally produced miR165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage dependent manner. To investigate the global regulation of SHR and SCR in the root, direct and indirect target genes of SHR and SCR were cross-compared with selected cell type specific expression profiles in the Arabidopsis root published in Birnbaum et al. (2003), Nawy et al. (2005), Lee et al. (2006), and Brady et al. (2007) [pubmed IDs: 14671301, 15937229, 16581911, 17975066]. Furthermore, the mature endodermis specific transcript profiles were generated using a GFP marker line, E30, and used together with published profiles in this comparison.
2010-04-27 | E-GEOD-16469 | biostudies-arrayexpress
Project description:This work studies the impact of AtNIGT1/HRS1-GR entrance in the nucleus upond DEX treatment in protoplasts. AtNIGT1/HRS1 TARGET. The whole procedure has been performed as previously described in Bargmann et al Mol Plant 2013. In brief, the protoplasts were transfected with the plasmid pBeaconRFP_GR-HRS1 that trigger the expression of HRS1 protein fused with the glucocorticoid receptor under control of CaMV35S promoter. Protoplasts were treated with 35µM cycloheximide (CHX) to inhibit translation and to select only direct target genes and 10µM dexamethasone (DEX) to induce HRS1-GR entry in the nucleus. Nitrate is maintained during the whole TARGET procedure. The Red Fluorescent Protein was used as marker selection for fluorescent-activated cell sorting (FACS) of successfully transformed protoplasts. RNA were extracted and amplified in order to be tested with ATH1 Affymetrix™ chips.
2015-01-05 | E-GEOD-64352 | biostudies-arrayexpress
Project description:One of the major barriers to understanding the control of T cell infiltration into target tissues has been the inherent difficulty in capturing the key variable of time in this process. Time is a critical variable, given that T cells are actively homing towards and infiltrating into target organs, and are concordantly evolving a highly pathogenic transcriptional program. Without understanding the time-dependency of T cell infiltration, we cannot fully comprehend key drivers and their dynamics. Here, we have been able to deconvolute time as a variable during T cell infiltration and tissue destruction during primate aGVHD by applying Serial Intravascular Staining (‘SIVS’) and pairing this with multiparameter flow cytotmetric and single-cell transcriptomic analysis. We also demonstrate significant overlap between NHP transcriptional signatures and those found in patients with active aGVHD, underscoring the clinical relevance of these findings.
2020-09-02 | GSE157280 | GEO
Project description:Primary cell wall (PCW) in plant mainly consists of three kinds of polysaccharides, cellulose, hemicellulose, and pectin. Although many genes encoding a variety of enzymes involved in synthesis, degradation, or modification of the PCW-related polysaccharides have been reported, regulation on expression of these PCW-related genes during PCW formation is still not fully understood. In this study, expression changes of PCW-related genes were analyzed during PCW regeneration in protoplasts. We used microarrays to reveal the global gene expression response against primary cell wall integrity stress during the primary cell wall regeneration in protoplasts.
2017-02-01 | GSE94348 | GEO
Project description:Transient genetic modification of plant protoplasts is a straightforward and rapid technique for the analysis of numerous aspects of plant biology. One drawback in the analysis of transformed protoplast suspensions is that they are a heterogeneous mix of cells that have and have not been successfully transfected. To overcome this problem, we have developed a system that employs a fluorescent positive selection marker in combination with flow cytometric analysis as well as fluorescence activated cell sorting (FACS) to isolate responses in the transfected protoplasts exclusively. This recombinase-compatible system enables high-throughput screening of genetic circuitry. Moreover, the use of FACS allows in depth downstream analysis. Lastly, over-expression is an effective means to dissect regulatory networks, especially where redundancy exists. Here, this system has been applied to the study of auxin signaling in order to investigate reporter gene activation and genome-wide transcriptional changes in response to manipulation of the auxin-response network. We have transiently over-expressed dominant negative mutant isoforms of Aux/IAA transcription factors (IAA7mII and IAA19mII; Tiwari et al., 2001) in Arabidopsis Pwer::GFP root protoplasts, making use of a RFP fluorescent positive selection marker and FACS to isolate the dually labeled (IAAnmII expressing and Pwer::GFP-positive) cells. We have compared the transcriptional differences between an empty vector control, IAA7mII and IAA19mII protoplasts that had either been treated with 5microM IAA or mock-treated for 3 hours. Keywords: hormone treatment, genetic modification
2009-03-01 | GSE13783 | GEO