Expression data from LCM-captured Arabidopsis root cells after challenge with Meloidogyne incognita
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Lauren McIntyre
PROVIDER: E-GEOD-37553 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Differential gene expression between groups of homogenous cell types is a biological question whose time has come. RNA can be extracted from small numbers of cells, such as those isolated by laser capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq. Recently, advances in amplification procedures make amplification directly from whole cell lysates possible. The aim of this study was to compare two amplification systems for variations in observed RNA abundance attributable to the amplification procedure for use with small quantities of cells isolated by laser capture microdissection. Arabidopsis root cells undergoing giant cell formation due to nematode infestation and un-infested control root cells were laser captured and used to evaluate 2 amplification systems. One, NuGEN's WT-Ovation Pico amplification system, uses total RNA as starting material while the other, NuGEN's WT-One-Direct Amplification system, uses lysate containing the captured cells. The reproducibility of whole genome transcript profiling and correlations of both systems were investigated after microarray analysis. The NuGEN WT-Ovation One-Direct system was less reproducible and more variable than the NuGEN WT-Ovation Pico system. The NuGEN WT-Ovation Pico Amplification kit resulted in the detection of thousands of genes differentially expressed genes between giant cells and control cells. This is in marked contrast to the relatively few genes detected after amplification with the NuGEN WT-Ovation One-Direct Amplification kit. Evaluation of each amplification system consisted of three biological replicates per treatment (control root cells or giant cells) with one biological replicate split into three technical replicates for a total of 10 samples per amplification procedure. RNA samples for amplification with the NuGEN WT-Ovation Pico kit were isolated from 150 control cells or from 80 giant cells using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). For amplification with the NuGEN WT-Ovation One-Direct kit, samples containing 150 control or 80 giant cells were collected directly into 2ul of the NuGEN lysis buffer. RNA amplifications were carried out according to the respective kitsâ?? protocols.
2010-06-08 | E-GEOD-21981 | biostudies-arrayexpress
Project description:The differentiation of specialized feeding sites in Zea mays root cells in response to nematode infestation involves substantial cellular reprogramming of host cells that is not well characterized at the molecular level. Expression data was generated from Zea mays root cells undergoing giant cell formation due to nematode infestation and from non-infested control root cells. Cells were laser captured 14 and 21 days after infestation. Each time point (14 day and 21 day) consisted of three biological replicates per treatment (control root cells or giant cells). Control cells were captured from an area ~13,000,000 um2 in size and giant cells were captured from an area ~5,000,000 um2 in size. RNA samples were isolated using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). RNA amplifications were carried out with the NuGEN WT-Ovation Pico kit.
2012-04-27 | E-GEOD-37556 | biostudies-arrayexpress
Project description:affy_pathogen_medicago - In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation, suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular levels. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules, followed by transcriptomic analysis, were performed. The RNA pools were extracted from these cells, amplified and used for transcriptomic studies with M. truncatula Affymetrix DNA chips. Keywords: organ comparison 12 arrays - Medicago infected with M. incognita or S. meliloti.
2012-03-01 | E-GEOD-19872 | biostudies-arrayexpress
Project description:affy_meloidogyne_rice2 - affy_meloidogyne_rice2 - Plant-parasitic nematodes cause heavy economic losses to global agriculture. The root knot nematode, Meloidogyne incognita, is an obligate parasite that causes significant damage to a broad range of host plants. M. incognita infection to dicotyledous plants is extensively studied but it is also important to study their interaction with monocotyledous plants, in particular with cereals. In our growing conditions, as of day 6, histological studies revealed a profound rice tissue reorganisation around nematodes, notably characterized by the plant feeding site formation. We are investigating the molecular plant response to M. incognita by carrying out a global analysis of gene expression during gall formation in rice, using giant cell-enriched root tissues at this early stage (6dpi) of gall development-Oryza sativa (var. Nipponbare) seedlings were grown on 6 cm3 SAP substrate completed with diluted Hoaglands solution (Reversat et al., 1999). Culture units were placed in a growth chamber illuminated with fluorescent tubes 9/24 h and maintained at 23°C for 6 days before being inoculated with a 300 J2-stage juveniles M. incognita. One day after inoculation (dai), the rice seedlings were immersed in de-ionised water to remove all J2s that had not penetrated the roots and allowing synchronization of the infection. Each seedling was transferred to a hydroponic mini chamber (Reversat et al., 2004). Sampling was performed at 6 dai and each of them contained galls from 45 infected plants, they were then hand-dissected, frozen in liquid-nitrogen and stored at -80°C. As reference samples, uninfected meristematic root fragments were dissected from seedlings grown under the same conditions. Each sample was replicated 3 times. Keywords: normal vs disease comparison 6 arrays - rice
2011-09-24 | E-GEOD-21772 | biostudies-arrayexpress
Project description:111,556,278 high-quality reads were obtained by a deep-sequencing approach that show an exact match to the genome of Meloidogyne incognita from the library of J2 juveniles of M. incognita (Mi). Based on these Solexa reads, 89 M. incognita microRNA genes were identified, which grouped into 67 non-redundant miRNAs with mature sequences. All of these candidate miRNAs were confirmed by qRT-PCR, and 26 of them could be detected in the library of the galls of cucumber root infected by M. incognita (GC). MiR-100 was found in a cluster with let-7, which is similar with B. malayi, a human parasitic nematode. Based on the results of deep sequencing, the expression of miR-100 was much more abundant than that of let-7, which indicated that they may not be co-expressed. The ortholog of let-7, a key regulator that controls the nematode from L4 to adult in C. elegans, could be frequently sequenced in the GC library, the later stages of development of M. incognita, while it had a relative low expression level in J2, which indicated that let-7 may have a similar role in the development regulation in plant parasitic nematodes. Frequently sequenced microRNAs, including miR-71, miR-100 and miR-124, should play an important role in the growth and proliferation of M. incognita. Identifying microRNAs of M. incognita based on deep-sequencing of the small RNAs of an Mi library, the J2 juveniles, and comparing their expression levels with those in a GC library, the gall of cucumber root infected with M. incognita.
2011-07-21 | E-GEOD-24833 | biostudies-arrayexpress
Project description:affy_meloidogyne_rice - affy_meloidogyne_rice - Plant-parasitic nematodes cause profound economic losses to global agriculture with the obligate sedentary endoparasitic varieties; amongst them the cyst and Root Knot Nematode (RKN) species are the most damaging. Meloidogyne graminicola is a RKN mainly found in the monocotyledous plants. In the compatible interaction with Oryza sativa, M. graminicola induces the characteristic formation of hook-like galls resulting from the redifferentiation of root cells into multinucleate giant cells. In order to understand the global transcriptome changes occurring during infection, several recent microarray studies on root knots have demonstrated complex changes in host plant gene expression in response to infection. However, to our knowledge, all these transcriptome studies were performed on dicotyledous plants. A histological study enabled us to observe hyperplasia and hypertrophy of the surrounding cells leading to the formation of hook-like galls. We also investigated the plant response to M. graminicola by carrying out a global analysis of gene expression during gall formation in rice, using giant cell-enriched root tissues at an early stage (2dpi) and a latter stage (4dpi) of gall development.-Oryza sativa (var. Nipponbare) seedlings were grown on 6 cm3 SAP substrate completed with diluted Hoaglands solution (Reversat et al., 1999). Culture units were placed in a growth chamber illuminated with fluorescent tubes 9/24 h and maintained at 23°C for 5 days before being inoculated with a 100 J2-stage juveniles M. graminicola. One day after inoculation (dai), the rice seedlings were immersed in de-ionised water to remove all J2s that had not penetrated the roots and allowing synchronization of the infection. Each seedling was transferred to a hydroponic mini chamber (Reversat et al., 2004). Sampling was performed at 2 and 4 dai and each of them contained galls from 70 infected plants, they were then hand-dissected, frozen in liquid-nitrogen and stored at -80°C. As reference samples, uninfected meristematic root fragments were dissected from seedlings grown under the same conditions. Each sample was replicated 3 times. Keywords: normal vs disease comparison,time course 9 arrays - rice
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