Comparison of gene expression profiles in diploid and transformed tetraploid MEF cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Xiwei Wu
PROVIDER: E-GEOD-18802 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:This SuperSeries is composed of the following subset Series: GSE18802: Comparison of gene expression profiles in diploid and transformed tetraploid MEF cells GSE18814: Comparison of DNA methylation profiles in diploid and transformed tetraploid MEF cells Refer to individual Series
2012-04-29 | E-GEOD-18815 | biostudies-arrayexpress
Project description:The aim of this study was to analyze the impact of autotetraploidy on gene expression in Arabidopsis thaliana by comparing diploid versus tetraploid transcriptomes. In particular, this included the comparison of the transcriptome of different tetraploid A. thaliana ecotypes (Col-0 vs. Ler-0). The study was extended to address further aspects. One was the comparison of the transcriptomes in subsequent generations. This intended to obtain information on the genome wide stability of autotetraploid gene expression. Another line of work compared the transcriptomes of different diploid vs. tetraploid tissues. This aimed to investigate whether particular gene groups are specifically affected during the development of A. thaliana autotetraploids. Samples 1-8: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 9-12: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 13-24: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 25-32: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 33-36: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Ler-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 37-40: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Col-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 41-44: Arabidopsis thaliana Col-0/Ler-0 diploid transcriptome. Transcriptional profiling and comparison of diploid Col-0 vs. diploid Ler-0 seedlings. The experiment was carried out with pedigree of esrablished lines. Samples 45-48: Arabidopsis thaliana Col-0/Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid Col-0 vs tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 and Ler-0 lines.
2010-05-01 | GSE18482 | GEO
Project description:Tetraploidisation has been implicated in tumorigenesis and in aneuploidy which is frequently observed in most human cancers. In this study we aim to reveal differences in gene expression profile of p53 defective isogenic diploid and tetraploid cell populations. Isogenic DLD1 populations were obtained by transient Dihydro-Cytochalasin B treatment and cell sorting of pure diploid and tetraploid populations by cell cycle profile several days after release from DCB. RNA isolation: Two technical replicas were collected for each population from two different passages (biological replicas) of 60-80% confluent cells.
2014-04-22 | E-MTAB-1789 | biostudies-arrayexpress
Project description:We propose that abnormal DNA content in tetraploid cells can alter the gene expression profile, contributing to the cellular transformation. To test this hypothesis, we employ mRNA microarray to compare the gene expression profile in transformed tetraploid cells with that in the parent diploid cells. Keywords: gene expression profile determination
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Project description:Genetically unstable tetraploid cells can promote tumorigenesis. Recent estimates suggest that ~37% of human tumors have undergone a genome-doubling event during their development. This potentially oncogenic effect of tetraploidy is countered by a p53-dependent barrier to proliferation. However, the cellular defects and corresponding signaling pathways that trigger growth suppression in tetraploid cells are not known. Here we combine genome-scale RNAi screening and in vitro evolution approaches to demonstrate that cytokinesis failure activates the Hippo tumor suppressor pathway in cultured cells as well as in naturally occurring tetraploid cells in vivo. Induction of the Hippo pathway is triggered in part by extra centrosomes, which alter small G-protein signaling and activate LATS2 kinase; LATS2 in turn stabilizes p53 and inhibits the transcriptional regulators YAP and TAZ. These findings define an important tumor suppression mechanism. Furthermore, our experiments uncover adaptations that allow nascent tumor cells to bypass this inhibitory regulation. Hepatocytes of newborn mice are initially diploid, but become progressively tetraploid with age. To study the mechanism of cell cycle arrest in naturally occurred tetraploidy, we used microarrays to detail the overall gene expression profile of diploid and tetraploid primary hepatocytes and identified YAP target genes up-regulated in diploid cells.
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Project description:To determine the differential expression of proteins in leaf and fruit of diploid and tetraploid watermelon
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Project description:The CMVpp65 protein contains 2 bipartite nuclear localization signals (NLS) at 415-438aa and 537-561aa near the carboxy terminus of CMVpp65 and a phosphate binding site related to kinase activity at lysine-436. A mutation of pp65 having K436N (CMVpp65mII) and further deletion of aa537-561 resulted in a novel protein (pp65mIINLSKO) that is kinase-less and has markedly reduced nuclear localization. The purpose of this report was to study the biologic characterization of this protein and its immunogenicity compared to native pp65.Using RNA microarray analysis, expression of the CMVpp65mIINLSKO had less effect on cell cycle pathways than did the native CMVpp65 and a greater effect on cell surface signalling pathways involving immune activity. It is concluded that the removal of the primary NLS motif from pp65 does not impair its immunogenicity and may actually be advantageous in the design of a vaccine. Keywords: comparison of cellular response to wild-type gene expression vs a mutated gene. The MRC-5 cells were transduced in triplicate, with rAAVintA, rAAVpp65N, rAAVpp65NLSKO for 48hrs and the total RNA was purified with RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay. After ribosomal RNA reduction (Invitrogen, Carlsbad, CA) to remove most of the 18S and 28S rRNAs, the GeneChip WT (whole transcript) cDNA Synthesis Kit, WT cDNA Amplification Kit, and WT Terminal Labeling Kit (Affymetrix, Inc., Santa Clara, CA) were used for target preparation. Ten µg of cRNA (antisense RNA) were added to the second-cycle cDNA reaction followed by fragmentation and Terminal Labeling process. The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 1.0 ST arrays. The Genechip® Human Gene 1.0 ST array was chosen because it offers the whole transcript coverage consisting of 28,869 genes on the array by approximately 26 probes spread across the full length of the gene.
2009-01-30 | E-GEOD-14347 | biostudies-arrayexpress
Project description:Varied genes may be responsible for the functional differences of distinct subsets of T cells. As a result, it is possible that regulatory T cells and pathogenic T cells may display a different set of gene profile regulating their functional status. To identify genes contributing to the functional role of T cells, we used microarrays to examine the global gene expression in regulatory T cells, pathogenic T cells, and control non-regulatory, non-pathogenic T cells. BDC, N79, N206 and NR206 CD4+ T cells were cultured in RPMI medium plus 5% fetal bovine serum in vitro. N206 and NR206 were used as Tregs, BDC were used as Tpath cells and N79 were used as neutral control cells . BDC, N79, N206 and NR206 were cultured for RNA extraction and hybridization on Affymetrix microarrays.
2011-01-06 | E-GEOD-26456 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE41309: Differential expression in response to water deficit in diploid leaves of sweet orange scion grafted alternatively on a diploid or auto-tetraploid Rangpur lime rootstock: data concerning the scion grafted onto diploid rootstock. GSE41310: Differential expression in response to water deficit in diploid leaves of sweet orange scion grafted alternatively on a diploid or auto-tetraploid Rangpur lime rootstock: data concerning the scion grafted onto tetraploid rootstock Refer to individual Series
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