SAGE analysis of maize root segments
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
SUBMITTER: Mark Fredricksen
PROVIDER: E-GEOD-25761 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Dark-grown maize seedlings with primary roots 12-20 mm in length were transplanted to high (-0.03 MPa) water potential vermiculite. About 1,000 roots were collected. Each root was divided into 4 segments (distances are from the junction of the root apex and root cap): segment 1, 0-3 mm plus the root cap; segment 2, 3-7 mm; segment 3, 7-12 mm; segment 4, 12-20 mm. Details of the conditions and nutrient modifications have been described before (Sharp et al., 1988; Spollen et al, 2000). From each segment, 250 mg of material was used and RNA was isolated form the combined sample containing all four segments. RNA was isolated using the RNeasy Maxi Kit (Qiagen). RNA integrity was verified by denaturing agarose gel electorphoresis and spectrophotometry.
2010-12-01 | GSE25761 | GEO
Project description:The root cap surrounds the root meristem, protecting it from harsh environments and facilitating root movement through soil. In Arabidopsis, new root cap cells produced in the meristem displace older cells toward the root periphery, where they undergo programmed cell death and are released from the root. This rapid cell turnover is a unique feature of the root cap and is modulated in part by the combined action of four NAC transcription factors, as well as cell wall modification enzymes. Here we show that the transcription factor NIN-LIKE PROTEIN 7 (NLP7) regulates root cap maturation in Arabidopsis by modulating expression of each of the NAC TFs as well as several cell wall modifying enzymes. NLP7 is a homolog of NIN, a transcription factor required for nodulation in Lotus japonicas, and is highly expressed in the columella root cap. Mutants have altered columella root cap development and decreased levels of homogalacturonan, a major component of pectin. Reverse genetic analysis of genes differentially expressed in nlp7 roots showed that two cell wall modifying enzymes, CELLULASE5 and XTH5, modulate root cap maturation likely downstream of NLP7. Plant cell wall modification is critical for nodulation, and we propose that this characteristic is also present in NLPs. We used microarrays to identify the differences in gene expression between whole roots of WT and nlp7-1 Arabidopsis plants Roots were cut at the root/hypocotyl junction and collected into RLT buffer in the RNeasy plant mini kit. Approximately 60 roots were collected per replicate, with two biological replicates. RNA was extracted using the RNeasy Micro Kit. Probes for array analysis were preparedfrom 1μg total RNA with the one-cycle amplification protocol by Affymetrix according to the manufacturer's instructions. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Arabidopsis Whole Genome ATH1 Affymetrix GeneChips.
2016-07-31 | E-GEOD-63474 | biostudies-arrayexpress
Project description:The root cap surrounds the root meristem, protecting it from harsh environments and facilitating root movement through soil. In Arabidopsis, new root cap cells produced in the meristem displace older cells toward the root periphery, where they undergo programmed cell death and are released from the root. This rapid cell turnover is a unique feature of the root cap and is modulated in part by the combined action of four NAC transcription factors, as well as cell wall modification enzymes. Here we show that the transcription factor NIN-LIKE PROTEIN 7 (NLP7) regulates root cap maturation in Arabidopsis by modulating expression of each of the NAC TFs as well as several cell wall modifying enzymes. NLP7 is a homolog of NIN, a transcription factor required for nodulation in Lotus japonicas, and is highly expressed in the columella root cap. Mutants have altered columella root cap development and decreased levels of homogalacturonan, a major component of pectin. Reverse genetic analysis of genes differentially expressed in nlp7 roots showed that two cell wall modifying enzymes, CELLULASE5 and XTH5, modulate root cap maturation likely downstream of NLP7. Plant cell wall modification is critical for nodulation, and we propose that this characteristic is also present in NLPs. We used microarrays to identify the differences in gene expression between whole roots of WT and nlp7-1 Arabidopsis plants
2016-07-31 | GSE63474 | GEO
Project description:We examine the development of the seedling roots based on two sets of data: one includes segments of the roots and one includes laser capture microdissection (LCM) root tissues.
2024-06-20 | GSE178534 | GEO
Project description:We developed a method to synchronize the induction of lateral roots in primary and adventitious roots of Zea mays, and used it to perform a genome-wide transcriptome analysis of the pericycle cells in front of the phloem poles during lateral root initiation. Lateral roots were induced in primary and adventitious roots of Maize. For the primary root, plants were germinated and grown 64 hours in NPA 50 µM, and then transfered to NAA 50 µM. For the adventitious roots, plants were germinated and grown in water for 6 days, then tranfered 4 days in NPA 25 µM, and finally transfered to NAA 25 µM. For all these roots, pericycle cells located in front of the phloem poles in segments of roots located between 5 and 10 mm distance from the root tip were isolated using laser capture microdissection after cryosection. Material was sampled at 0 hours (NPA) and after 2, 3 and 4 hours of NAA treatment, for both the primary and adventitious roots and also after 6 hours and 9 hours of NAA treatment for the adventitious roots.
2013-07-16 | E-GEOD-45691 | biostudies-arrayexpress
Project description:The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap-specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture. To further explore the specificity of naxillin for lateral root development, we compared the early effects of naxillin at the transcriptome level with NAA (1-Naphthaleneacetic acid) in roots of 3-day-old seedlings after 2-h and 6-h treatment.
2012-12-18 | GSE42896 | GEO
Project description:The root cap-specific conversion of the auxin precursor indole-3-butyric acid (IBA) into the main auxin indole-3-acetic acid (IAA) generates a local auxin source which subsequently modulates both the periodicity and intensity of auxin response oscillations in the root tip of Arabidopsis, and consequently fine-tunes the spatiotemporal patterning of lateral roots. To explore downstream components of this signaling process, we investigated the early transcriptional regulations happening in the root tip during IBA-to-IAA conversion in Col-0 and ibr1 ibr3 ibr10 triple mutant after 6 hours of IBA treatment. Arabidopsis thaliana (L). Heynh., Col-0 and ibr1ibr3ibr10 seeds were germinated vertically on solid medium derived from standard Murashige and Skoog (MS) medium. Three days after germination, Col-0 and ibr1ibr3ibr10 seedlings were transferred to a fresh MS medium supplemented with or without 10 ?M indole-3-buytric acid (IBA) for 6 hours. Then, root tip segments (~4mm) were dissected from the primary root and harvested for further RNA extraction. For each treatment, at least 120 individual Col-0 or ibr1ibr3ibr10 mutant root tip segments were sampled and three independent biological replicates were performed. Hormone and DMSO solution were filer-sterilized before being added to the medium.
2015-05-12 | E-GEOD-59426 | biostudies-arrayexpress
Project description:The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap-specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture. To further explore the specificity of naxillin for lateral root development, we compared the early effects of naxillin at the transcriptome level with NAA (1-Naphthaleneacetic acid) in roots of 3-day-old seedlings after 2-h and 6-h treatment. Arabidopsis thaliana (L). Heynh., Col-0 seeds were germinated vertically on solid medium derived from standard MS medium supplemented with 10 μM NPA (1-N-Naphthylphthalamic acid). Three days after germination, plants were transferred to 10 μM NAA (1-Naphthaleneacetic acid) or 50 μM naxillin for 2 and 6 hours. Plants were sampled before (Roots at T0, NPA) or after treatment (Roots at T1 and T2). RNA isolation was performed on 500 root sections (only root without meristems) for each sample. All sampling points were performed in three independent experiments.
2012-12-18 | E-GEOD-42896 | biostudies-arrayexpress
Project description:The cotyledons of etiolated seedlings from terrestrial flowering plants must emerge from the soil surface, while roots must penetrate the soil to ensure plant survival. We show here that the soil emergence related transcription factor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) regulates root penetration via transducing external signals perceived by the receptor kinase FERONIA (FER) in Arabidopsis thaliana. The loss of FER function in the fer-4 mutant resulted in a severe defect in root penetration into hard soil or medium. Single-cell RNA-seq profiling of roots revealed a distinct cell clustering pattern, especially for root cap cells, and revealed PIF3 as a putative FER-regulated transcription factor. Biochemical, imaging, and genetic experiments confirmed that PIF3 is required for root soil penetration. Moreover, FER interacted with and stabilized PIF3, which then modulated the expression of mechanosensitive ion channels and the sloughing of outer cells in the root cap. We propose a novel mechanism of soil penetration by plant roots.
2023-12-31 | GSE225299 | GEO
Project description:The root apex is an important section of the plant root, involved in environmental sensing and cellular development. Analyzing the gene profile of root apex in diverse environments is important and challenging, especially when the samples are limiting and precious, such as in spaceflight. The feasibility of using tiny root sections for transcriptome analysis was examined in this study.To understand the gene expression profiles of the root apex, Arabidopsis thaliana Col-0 roots were sectioned into Zone-I (0.5 mm, root cap and meristematic zone) and Zone-II (1.5 mm, transition, elongation and growth terminating zone). Gene expression was analyzed using microarray and RNA seq.Both the techniques, arrays and RNA-Seq identified 4180 common genes as differentially expressed (with > two-fold changes) between the zones. In addition, 771 unique genes and 19 novel TARs were identified by RNA-Seq as differentially expressed which were not detected in the arrays. Single root tip zones can be used for full transcriptome analysis; further, the root apex zones are functionally very distinct from each other. RNA-Seq provided novel information about the transcripts compared to the arrays. These data will help optimize transcriptome techniques for dealing with small, rare samples.
2018-10-29 | GSE115486 | GEO