Microarrays of Female and Male cyst nematode infected Arabidopsis root samples
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Shahid Siddique
PROVIDER: E-MTAB-8648 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Background; Heterodera schachtii is an economically important plant parasitic nematode that forms a syncytium from a cell superficial to the formed vascular bundle by progressive recruitment of other cells into the structure. The pattern of plant gene expression changes dramatically inside the syncytium. The pathogen probably plays a major role in defining the plant response by choice of initial plant cell during precise behaviour in planta and/or by the secretions it releases. The modified plant cells enable a high feeding rate by the female nematode so enhancing its rate of development and subsequent daily egg production. Arabidopsis is widely used as a model plant to characterise molecular responses to nematodes (e.g. Sijmons et al., 1991 Plant J. 1:245-254.). A complete overview of the changes in plant gene expression when sedentary nematodes establish has not yet been gained using Arabidopsis or any other host plant. Experimental Approaches; Our initial studies will focus on the H. schachtii/Arabidopsis interaction. To assure reliable microarray screening care has been taken to minimise extraneous differences between samples (see "Growth conditions" section). At 21 days (Growth stage 3.2-3.5 Boyes et al., 2001 Plant Cell 13:1499-1510) Arabidopsis plants were challenged with rigorously sterilised, infective nematodes of H. schachtii as before (Urwin et al., (1997) Plant Journal 12: 455-461.). 35 sterile J2s were pipetted onto small ~0.5mm2 squares of sterile GF/A filter paper. The GF/A paper was left in direct contact with the zone of elongation on 3 lateral roots per plant for 48 hours. Control plants were mock inoculated with sterile water. Sections of root containing syncytia have been excised from the thin and transparent roots of Arabidopsis and collected into RNAlater solution (Ambion) at 21 days post infection (Growth Stage 6.1 Boyes et al. 2001). The female nematode has been removed with watch-maker's forceps. Equivalent sections of root have been harvested from non-infected plants. Material has been collected from c. 1000 plants for each of the two samples and the uninfected material serves as an internal control. Total RNA has been prepared from the reference and test root material using an RNeasy plant RNA preparation kit (Qiagen) according to methods required by GARNET.Some questions on the form are omitted as we are not using mutant or transgenic lines. This is our first application. Experimenter name = Peter Edward Urwin; Experimenter phone = 0113 343 3035/2909; Experimenter fax = 0113 343 3144; Experimenter address = Centre for Plant Science; Experimenter address = University of Leeds; Experimenter address = Leeds; Experimenter zip/postal_code = LS2 9JT; Experimenter country = UK Experiment Overall Design: 2 samples were used in this experiment
2008-06-14 | E-GEOD-5724 | biostudies-arrayexpress
Project description:To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke. Forty-two Sprague-Dawley rats were subjected to: 2 hours of middle cerebral artery occlusion (MCAO); a permanent-MCAO; or were used as controls. tPA was administered to half of the rats in each group at 3hours. Whole blood was drawn at 24 hours, and isolated RNA levels measured on Affymetrix Rat Genome 230 2.0 GeneChip microarrays to examine the entire RNA transcriptome. 42 samples, 7 groups in total ( 2 treatmented disease, 2 untreated disease, and 3 control groups), each group had 6 replicates
2014-03-29 | E-GEOD-21136 | biostudies-arrayexpress
Project description:Tissue samples in biobanks preserved by formalin-fixation and paraffin-embedding (FFPE) and/or optimal cutting temperature (OCT)-embedded and subsequently freezing are highly valuable in experimental studies where the results can be related to clinical parameters. Today, mass spectrometry (MS)-based proteomics is the method of choice for unbiased and relative comparison of the abundances of thousands of proteins present in biological samples. MS analysis of FFPE- and OCT-preserved tissue has been limited, but it is now approachable using newly developed protocols. However, it has not been clarified how the results from different preservation methods agrees and differ. In this study, we use a unique sample set of urinary bladder cancer tissues of two different tumor stages (Ta/T1 – non-muscle invasive and T2/T3 muscle invasive); upon sampling the tumors were divided and preserved by the two methods. Thereafter a protocol for parallel processing of the samples were applied after which the samples were analyzed with label free quantitative MS analysis. Over 700 and 1200 proteins were quantified in FFPE and OCT samples, respectively. Principal component analysis showed that the largest differences between samples are based on the preservation method, but this analysis could also classify the tumors into different stages in each preservation. The overlap of quantifiable proteins between the preservation methods were 84% when all proteins and full data set were taken into consideration, but only 41% on average when proteins from a specific tumor were analyzed. Proteins involved in mitochondrial function were overrepresented among proteins present in OCT data but missing in the FFPE data, indicating that these proteins are not well preserved by FFPE. Moreover, univariate analysis showed that HMGCS2 protein is uniquely quantified in Ta/T1 tumors in both FFPE and OCT data, and that LGALS1, ANXA5 and plastin proteins are upregulated in T2/T3 tumors compared to Ta/T1 tumors in both FFPE and OCT data, confirming the consistency between the data sets and suggesting these proteins as biomarkers. Finally, LGALS1 data were verified by immunohistochemistry staining of an independent data set.
2021-09-09 | PXD020194 | Pride
Project description:The objective of this study was to make use of gene expression signatures and functional assays to delineate differences between various intestinal colon carcinoma cell lines and normal intestinal epithelium to assess their appropriateness as a tumor model or for drug absorption studies. [Cell lines] Total RNA of biological replicate samples (i.e.different passages) from a panel of cell lines was collected and resulting amplified cRNA hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays. Samples are labeled as follows: SampleNumber_CellLine. [Laser dissected tumor cells (LDM)] Total RNA of three different samples laser dissected tumor cells, normal colonocytes, and enterocytes of ileum and two samples of jejunum was collected and resulting amplified cRNA hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays. Samples are labeled as follows: SampleNumber_TissueType_Origin.
2012-06-23 | E-GEOD-30292 | biostudies-arrayexpress
Project description:Alternative splicing analysis of laser micro-dissected lung dysplasia RNA samples Lung dysplasia is a precancerous condition with high risk of malignant transformation. Little is known about alternative spliced (AS) genes in dysplasia. We therefore investigated laser micro-dissected microscopic foci of non-contaminant dysplasia and/or lung adenocarcinoma of c-Raf transgenic mice and searched genome wide for AS genes using exon arrays. Notably, bioinformatics defined 34 and 36 AS genes in the comparison dysplasia versus transgenic unaltered and non-transgenic lung tissue while the comparison adenocarcinoma versus transgenic unaltered and non-transgenic lung tissue revealed 54 and 56 genes, respectively. So far only 6 of these were reported for lung cancer. Importantly, dysplasia related AS genes were also regulated in lung cancer to suggest a role in disease onset. Next to exon skipping/inclusion alternative splicing at the 3M-bM-^@M-^Y and 5M-bM-^@M-^Y was common and included genes of the splicing regulatory pathway. Disease dependent changes of variant transcripts were confirmed by RT-PCR while Western blotting identified alternative splicing to modulate protein levels of AS genes. For the AS genes Add3, Cast, Osbpl6, Nedd4l, Numb, Picalm and Slk transcript and protein level agreed well, whereas for Arhgef11, Clstn1, Dlg1, Dock9, Mbnl2, Mfge8, Npnt, Pdlim5, Ppp2r5c, Tjp1 notable differences in the abundance of variant transcripts were observed by RT-PCR and gel electrophoresis. Moreover, expression of individual variants differed between dysplasia and carcinoma to suggest their disease dependent regulation. Western blotting of IQGAP1, MYO6, PTPRM, RABGAP1L and RAD50 confirmed significant regulation of isoforms in lung cancer as compared to non-transgenic, transgenic unaltered and dysplastic lung tissue. For 46 AS genes expression of the non-variant protein was reported in human lung cancer (www.proteinatlas.org) and for 13 of these, cancer related AS events are known. Overall, new insight into lung dysplasia was obtained with 43 new cancer related AS genes to aid diagnosis and molecular intervention strategies. We analyzed and compared dysplastic (n=4) and adenocarcinoma (n=4) lesions and with transgenic but unaltered (n=4) and non-transgenic (n=5) lung tissue obtained from SPC/c-Raf transgenic mice with aid of laser micro dissection pressure catapulted (LMPC) technique. Dysplasia is a pre-neoplastic condition and developed at 5 month of age in the proposed mouse model. LMPC provides precise microscopic lesion collection without contamination. The RNA samples were analyzed using the Affymetrix Mouse Exon 1.0 ST platform. Alternative splicing was analyzed using Biotique XRAY tool. No technical replicates were performed.
2014-06-23 | E-GEOD-38948 | biostudies-arrayexpress
Project description:30 patients were randomized equally into three groups: no treatment, bicalutamide (antiandrogen) 150 mg daily, and goserelin (GnRH agonist) 3.6 mg every 4 weeks. Following the neoadjuvant treatment for 12 weeks, patients underwent radical prostatectomy. Freshly frozen specimens were collected for expression profiling using Illumina microarray (probes for >25 000 mRNAs) <br><br>A file containing processed data is available on the FTP site for this experiment.
2012-03-01 | E-MEXP-3081 | biostudies-arrayexpress
Project description:Plasmacytoid dendritic cells (pDCs) are scarcely present in the inflamed human atherosclerotic plaque, where they are presumed to exert pro-inflammatory functions through release of type I interferons. However, the precise role of pDCs in human atherosclerosis yet remains to be established. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. We investigated the impact of human plaque pDCs on its local context, applying state of the art transcriptomics analysis on Laser Capture Microdissected fractions of human atherosclerotic plaques, distinctively enriched in pDCs, or pDCs-void.
2013-08-26 | E-GEOD-49670 | biostudies-arrayexpress
Project description:A data set of normal epithelium, serous ovarian surface epithelial-stromal tumors (benign and type II malignancies), stroma distal to tumor, and stroma adjacent to tumor (50 samples total). Additional cel files are included which represent replicate sampling from patients, and cel files that failed quality control but may be bioinformatically interesting. Additional replicate or failed cel files were not included in the final analysis (and so these samples were not included in the matrix). Background: Ovarian cancer is the most lethal gynecologic cancer in the United States. If caught in early stages, patient survival rate can reach 94%, when diagnosed at late stages survival rates drop to 28%. Correct diagnosis depends on the presence of definite symptoms: while ~90% of diagnosed ovarian cancers have symptoms, they tend to be unfocused and subacute. A definitive and early molecular signature of disease is thus desired. To further progress towards this goal, we present an Affymetrix™ human exon array data set measuring ovarian tumor expression, assembled using best practices. Method: Samples were collected from patients with benign and malignant (type II) serous ovarian surface epithelial-stromal tumors. Normal epithelium, tumor, stroma adjacent to tumor, and distal stroma were selected based on histopathology, and isolated using laser capture microdissection. Nugen products were used to perform random-primed mRNA amplification procedures (for full transcript capture) before hybridization to Affymetrix exon chips. Tumor expression and paracrine signaling was assessed using GC-RMA and a two-way Model I ANOVA. Single enrichment ontological analysis and gene network construction were performed to guide inferences about biological context. Results: In total, across 50 microarrays, ~270 million measurements were obtained. Based on comparisons to known ovarian cancer properties as established in molecular genetics literature, the initial analysis presented emphasizes data quality. Major trends between sample classes included: apical surface and tight junction activity, mitotic activity, benign tumor suppression, epithelial-mesenchymal transitioning, tumor oncogene activity, and paracrine signaling. A list of differentially expressed transcripts has been produced to enable rapid comparisons with published biomarker lists, but it is expected that detailed alternative transcript analysis will refine these predictions. Conclusions: A data set of 50 arrays, from carefully dissected serous ovarian surface epithelial-stromal tumors, has been produced, from which high quality measurements were obtained. While relatively small in number, this represents an important addition to the community pool of ovarian tumor samples, and the chosen platform enables bridging between 3' expression and exome sequencing data sets. This represents a significant contribution to the ovarian cancer genetics community. A total of 50 human ovary samples were used in analysis: 23 tissue samples laser capture microdissected from an ovary with a benign serous tumor (specifically 4 normal epithelium samples, 5 tumor samples, 6 stroma samples adjacent to the tumor, and 8 stroma samples distal of the tumor), and 27 tissue samples laser capture microdissected from an ovary with a malignant serous tumor (specifically 5 normal epithelium samples, 8 tumor samples, 7 stroma samples adjacent to the tumor, and 7 stroma samples distal of the tumor). Additional cel files were provided which, although were used in the quality control of the data set, were not used in the final experimental analysis. 8 replicates are included as cel files (1 from each cohort previously listed). 14 cel files were also included which failed quality control. Although the replicate and failed cel files were not used in the final analysis, they may still be interesting in other research.
2011-05-11 | E-GEOD-29156 | biostudies-arrayexpress
Project description:Tongue squamous cell carcinoma (TSCC) varies in characteristics even in early stages and is mainly classified into three subtypes, which are superficial, exophytic and endophytic types, based on a macroscopic appearance of tumor growth.Of these subtypes, endophytic tumor has a poorer prognosis because of its invasive feature and higher frequency to have metastasis. To understand a molecular mechanism of endophytic subtype and identify biomarkers, we performed comprehensive microarray analysis for mRNAs from clinical biopsy sampleswhich were classified into subtypes and found overexpression of parvin-beta (PARVB) gene significantly related to endophytic type. PARVB is known to play a critical role in actin reorganization and focal adhesions. Knocking down PARVB expression in vitrocaused apparent decreases in cell migration and wound healing, implying that PARVB has a crucial role in cellular motility. Moreover, metastasis-free survival was significantly lowered in patients with higher PARVB expression. Therefore overexpression of PARVB is a candidate biomarker for endophytic tumor and metastasis and may be clinically applicable for decision making of an adjuvant therapy in TSCC. Twenty seven OCT embedded tissues were used to extract total RNA. Then RNAs were amplified, biotinylated, fragmented and hybridized on GeneChip Human Genome U133 plus 2.0 arrays.
2015-12-31 | E-GEOD-52915 | biostudies-arrayexpress
Project description:IL13R?2 overexpression promotes metastasis of basal-like breast cancers IL13R?2 depletion in highly metastatic breast cancer cells suppresses lung metastases formation by upregulating TP63 and decreasing their migratory potential MCF10CA1a (MIV) cells expressing the luciferase gene (MIV-Luc), were stably transduced with lentiviral constructs expressing either scrambled shRNA or shRNA against IL13R?2. The two cell lines were then either mock treated or treated with 20ng/ml IL13 for 16h followed by RNA isolation. Gene expression analysis was performed using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool.
2015-07-28 | E-GEOD-57677 | biostudies-arrayexpress