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Genes differentially expressed in wild-type Medicago truncatula plants during nodulation

ABSTRACT: We used an Affymetrix oligonucleotide microarray consisting of 9,935 tentative consensus (TC)sequences, which are based on cDNA libraries (Mitra et al., 2004 [PMID:15220482]). We examined gene expression of wild-type M. truncatula plants after inoculation with wild-type S. meliloti at 1 d, 4 d, 7d, 14 d, and 21 d. We chose these time points because they span the range of development of the Rhizobium-legume symbiosis, from initiation of the interaction through nitrogen fixation. The gene expression data for the 1-day time point (Mitra et al., 2004 [PMID 15220482]) and the other time points was previously published (Starker el al., 2006 [PMID 16407449]).

ORGANISM(S): Medicago truncatula Sinorhizobium meliloti

PROVIDER: GSE28173 | GEO | 2011/03/26

SECONDARY ACCESSION(S): PRJNA143149

REPOSITORIES: GEO

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Genes differentially expressed in wild-type Medicago truncatula plants during nodulation

Project description:We used an Affymetrix oligonucleotide microarray consisting of 9,935 tentative consensus (TC)sequences, which are based on cDNA libraries (Mitra et al., 2004 [PMID:15220482]). We examined gene expression of wild-type M. truncatula plants after inoculation with wild-type S. meliloti at 1 d, 4 d, 7d, 14 d, and 21 d. We chose these time points because they span the range of development of the Rhizobium-legume symbiosis, from initiation of the interaction through nitrogen fixation. The gene expression data for the 1-day time point (Mitra et al., 2004 [PMID 15220482]) and the other time points was previously published (Starker el al., 2006 [PMID 16407449]). Three or five independent biological replicates were performed at each time point (1, 4, 7, 14 and 21 days after treatment) and each treatment (buffer and wild-type bacteria).

2011-03-26 | E-GEOD-28173 | biostudies-arrayexpress

Transcriptome profiling of liver samples from wild-type and Adamts12-/- mice in response to CCl4-induced liver injury.

Project description:We used Adamts12−/− and wild-type mice generated and genotyped by El Hour et al. 2010 (PMID: 20208563). eight-week-old females were treated by intraperitoneal injections of CCl4 (Sigma-Aldrich, St. Louis, MO, USA) diluted at 3% v/v in olive oil. A single dose of CCl4 0.3 ml/kg of mouse body weight was administered (acute treatment) and mice were sacrificed after 4h, 12h, 24h or 7 days. Control mice were treated with the vehicle (olive oil). Liver samples were collected, weighed and treated as previously described (Kesteloot et al. 2007, PMID: 17929299). We performed gene expression profiling analysis using data obtained from liver samples of wild-type or Adamts12_KO mice at different time points after CCl4 (or vehicle) injection.

2023-02-04 | GSE224052 | GEO

Differential gene expression of meiotic drive system of Aedes aegypti

Project description:We conducted a whole transcriptome analysis of testes from a meiotic drive-carrying strain (T37) in comparison with a drive-sensitive strain (RED) using microarrays based on the complete annotated Ae. aegypti gene set. The T37 strain, which carries a strong meiotic drive gene (Mori et al., 2004 (PMID 15605641)), was established from mosquitoes collected in Trinidad. The RED strain is highly sensitive to the meiotic drive gene (Hickey and Craig, 1966 (PMID ); Mori et al., 2004 (PMID 15605641)).

2015-07-15 | GSE43562 | GEO

Gene Expression Analysis of Transgenic Myc-Driven Liver Tumor Formation and Regression

Project description:Gene expression changes were examined in transgenic MYC-driven liver cancers at different time points as tumors formed and upon early regression. Time points evaluated include: Control (non-tumor bearing), Pre-tumor (mice were removed from doxyclycine in their diet to induce MYC oncogene expression for 4-5 weeks), Tumor (tumor nodules from mice that had been off of doxycycline for 8-9 weeks) and Early tumor regression (tumor-bearing mice were placed back on doxycycline for 72 hrs to inhibit MYC oncogene expresion). MYC-Driven Mouse Tumor Models are described in Schahaf, et al., Nature, 2004 and Goga, et al., Nature Medicine, 2007.

2011-07-06 | GSE28198 | GEO

IL-2 transfection of A673-cells

Project description:Response of A673-cells to transfection with interleukin 2 (IL-2). Ewing family tumor (EFT) cell line A673 was transfected with an expression vector for IL-2 (cell line SBVGA1) or empty control vector (cell line SBVGA3). Cells were harvested at 3 different time points and processed for DNA-microarray analysis using Affymetrix HG-U95A microarrays. Primary image analysis was performed using MAS 5.0. In addition, primary analysis was performed with MAS 4.0 and data were scaled to an target intesity of 200. These data have been analysed together with other published data that have been scaled to the same target intensity (see Staege et al. Pediatr Blood Cancer 2004 Jul;43(1):23-34. See also Staege et al. Cancer Res. 2004).

2004-10-11 | GSE1823 | GEO

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS: Twin blood plasma quantitative variance components

Project description:This data set represents a reanalysis of human blood plasma samples measured by SWATH-MS of 36 pairs of monozygotic and 22 pairs of dizygotic twins that were sampled at two longitudinal time points (Liu et al., 2015, PMID:25652787). The data were used to determine the overall quantitative variability of 4322 peptidoforms in the sample cohort and to assign the measured variability to heritability, environmental or longitudinal effects.

2017-06-06 | PXD004574 | Pride

Osteoblastic loss of Ezh2

Project description:Osteblastic loss of Ezh2 was achieved by breeding Ezh2flox/flox (Su et al., PMID: 12496962) with Osx-Cre (Rodda et al., PMID:16854976).

2018-07-25 | GSE111245 | GEO

Discovery of genes regulated by the metastasis suppressor gene, RhoGDI2

Project description:A number of studies find that metastasis suppressor proteins, including RhoGDI2, may function in part though controlling expression of genes regulating metastasis (reviewed in Smith and Theodorescu, Nature Reviews Cancer, 2009, PMID: 19242414). To uncover systematically gene expression patterns dependent on RhoGDI2 expression, we profiled gene expression in stably transfected control (GFP empty vector) UM-UC-3 bladder carcinoma cells (which have lost endogenous expression of RhoGDI2, as occurs commonly in the progression of bladder cancer PMID: 15173088), as well as stably transfected GFP-tagged RhoGDI2 expressing UM-UC-3 cells. References: Moissoglu K, McRoberts KS, Meier JA, Theodorescu D et al. Rho GDP dissociation inhibitor 2 suppresses metastasis via unconventional regulation of RhoGTPases. Cancer Res 2009 Apr 1;69(7):2838-44. PMID: 19276387 Wu Y, Moissoglu K, Wang H, Wang X et al. Src phosphorylation of RhoGDI2 regulates its metastasis suppressor function. Proc Natl Acad Sci U S A 2009 Apr 7;106(14):5807-12. PMID: 19321744 Smith SC, Theodorescu D. Learning therapeutic lessons from metastasis suppressor proteins. Nat Rev Cancer 2009 Apr;9(4):253-64. PMID: 19242414 Theodorescu D, Sapinoso LM, Conaway MR, Oxford G et al. Reduced expression of metastasis suppressor RhoGDI2 is associated with decreased survival for patients with bladder cancer. Clin Cancer Res 2004 Jun 1;10(11):3800-6. PMID: 15173088

2012-04-15 | GSE35014 | GEO

High-resolution translatome analysis reveals cortical cell programs during early soybean nodulation

Project description:The TRAP-seq process is dependent on the expression of a cell layer-specific His-FLAG-tagged ribosomal protein L18 (HF-GmRPL 18), which allows for the immunoprecipitation of ribosomes with their corresponding mRNA to produce tissue-specific translatomes (Zanetti et al., 2005; Castro‐Guerrero et al., 2016).To capture events occurring in the cortex during the early stages of infection and initial cortical cell divisions, we inoculated plants and performed a time-course collection of root samples at 72- and 96-hour post inoculation (hpi) followed by TRAP-seq. Immunoblot analysis indicated that an adequate amount of protein was present for immunoprecipitation. To study rhizobial-induced transcriptional changes in the cortex during early nodule development, we identified a soybean promoter (Glyma.18g53890, Figure 1B) expressed exclusively in the cortex cells using LCM (Kerk et al., 2003; Casson et al., 2008) followed by transcriptional analysis. The cortex-specific promoter was used to drive the expression of GmRPL18 in soybean hairy roots. To capture events occurring in the cortex during the early stages of infection and initial cortical cell divisions, we inoculated plants and performed a time-course collection of root samples at 72- and 96-hour post inoculation (hpi) followed by TRAP-seq. Immunoblot analysis indicated that an adequate amount of protein was present for immunoprecipitation (Figure 1C). Taken together, time-course cortex-specific TRAP-seq was established for studying of early nodule development in soybean.

2022-03-21 | GSE192785 | GEO

acute genes during CNS injury and their expression in cultured astrocytes

Project description:A robust set of CNS transcript changes was defined by comparing microarray data that describe the injury response of the rat retina [Vazquez-Chona et al., IOVS 2004; GSE1001], brain [Matzilevich et al., J Neurosci Res 2002; GSE1911], and spinal cord [Di Giovanni et al., Ann Neurol 2003; GDS63]. We determined the CNS injury genes that were expressed in cultured astrocytes from rat cortex [GSM34300] and from human optic nerve head [Yang et al., Physiol Genomics 2004; GDS532]. Keywords: other

2005-07-01 | GSE1928 | GEO

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