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Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE24877: Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs NA16) GSE24878: Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs COLONY) GSE24879: Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs. Tumor) Refer to individual Series

ORGANISM(S): Rattus norvegicus

SUBMITTER: Dr. Gopal Pande

PROVIDER: E-GEOD-24893 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs NA16)

Project description:Cell substrate adhesion plays an important role in cellular transformation of rat fibroblast cell lines, however a few viable non-adherent fibroblast cells when placed in suspension for a time period of 16 h (NA16) showed varied phenotypic characteristics like colony and tumor formation In order to understand the molecular events associated with adhesion independent cell survival ability of NA16, whole genome profiling was performed using Affymetrix Rat 230_2 GeneChips Keywords: Expression profiling of a adhesion deprived transformed cell line F111 fibroblast cell lines were grown in adhesion (A16) and suspension (NA16) conditions for 16h. These suspension cells (NA16) were plated on soft agar for colony formation and also injected in nude mice subcutaneously for tumor formation. A16 samples were considered as the control ones. Total RNA isolated from the samples (A16, NA16, Colony and Tumor) was subjected for expression analysis using Affymetrix Rat 230.2 GeneChip System. The experiment was repeated biologically and technically twice.

2010-11-14 | E-GEOD-24877 | biostudies-arrayexpress

Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs COLONY)

2010-11-14 | E-GEOD-24878 | biostudies-arrayexpress

Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs. Tumor)

2010-11-14 | E-GEOD-24879 | biostudies-arrayexpress

Rattus norvegicus

Project description:Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs NA16)

| PRJNA133417 | ENA

Rattus norvegicus

Project description:Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs. Tumor)

| PRJNA133421 | ENA

Rattus norvegicus

Project description:Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs COLONY)

| PRJNA133419 | ENA

Project description:Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation

| PRJNA132191 | ENA

Lipopolysaccharide modulates rhinovirus-induced chemokine secretion in monocytes and macrophages.

Project description:Rhinovirus (RV) infection has been shown to exacerbate asthma. Understanding of the underlying mechanisms by which RV infections provoke airway inflammation and remodeling in asthma may offer significant insight into asthma pathogenesis and exacerbations as well as offer opportunities for improved disease management. Expression analysis of RV A16-treated primary peripheral blood monocytes from human donors was performed to determine what pattern of gene expression is associated with RV infection of monocytes in vitro. Peripheral blood monocytes were isolated from 5 adults. Following overnight incubation in RPMI supplemented with 10% FBS, the monocytes were stimulated with purified major group RV A16 at multiplicity of infection of 10 plaque forming units (pfu) per cell or with growth media alone (mock). Cells were lysed 4 hours after treatment and isolated total RNAs were pooled per treatment and analyzed using the Affymetrix GeneChip HuGeneFL Array (Hu6800, Affymetrix, Santa Clara, CA).

2014-01-31 | E-GEOD-54558 | biostudies-arrayexpress

High complexity cellular barcoding and clonal tracing reveals stochastic and deterministic parameters of radiation resistance

Project description:It is elusive whether clonal selection of tumor cells in response to ionizing radiation (IR) is a deterministic or stochastic process. With high resolution clonal barcoding and tracking of over 400.000 HNSCC patient-derived tumor cells the clonal dynamics of tumor cells in response to IR was analysed. Fractionated IR induced a strong selective pressure for clonal reduction. This significantly exceeded uniform clonal survival probabilities indicative for a strong clone-to clone difference within tumor cells. Survival to IR is driven by a deterministic clonal selection of a smaller population which commonly survives radiation, while increased clonogenic capacity is a result of clonal competition of cells which have been selected stochastically. The ratio of these parameters is amenable to radiation sensitivity which correlates to prognostic biomarkers of HNSCC. Evidence for the existence of a rare subpopulation with an intrinsically radiation resistant phenotype was found at a frequency of 0.6-3.3%. With cellular barcoding we introduce a novel functional heterogeneity associated qualitative readout for evaluating the contribution of stochastic and deterministic clonal selection processes in response to IR.

2021-09-07 | E-MTAB-9693 | biostudies-arrayexpress

High complexity cellular barcoding and clonal tracing reveals stochastic and deterministic parameters of radiation resistance - Photon Irradiated samples

Project description:It is elusive whether clonal selection of tumor cells in response to ionizing radiation (IR) is a deterministic or stochastic process. With high resolution clonal barcoding and tracking of over 400.000 HNSCC patient-derived tumor cells the clonal dynamics of tumor cells in response to IR was analysed. Fractionated IR induced a strong selective pressure for clonal reduction. This significantly exceeded uniform clonal survival probabilities indicative for a strong clone-to clone difference. within tumor cells. Survival to IR is driven by a deterministic clonal selection of a smaller population which commonly survives radiation, while increased clonogenic capacity is a result of clonal competition of cells which have been selected stochastically. The ratio of these parameters is amenable to radiation sensitivity which correlates to prognostic biomarkers of HNSCC. Evidence for the existence of a rare subpopulation with an intrinsically radiation resistant phenotype was found at a frequency of 0.6-3.3%. With cellular barcoding we introduce a novel functional heterogeneity associated qualitative readout for evaluating the contribution of stochastic and deterministic clonal selection processes in response to IR. To analyze transcriptomic changes of HNSCC cell lines after fractionated Photon IR (5x4Gy), RNAseq analysis was performed on irradiated cells in comparison to untreated control cells (EBI submission E-MTAB-9693)

2021-08-31 | E-MTAB-10685 | biostudies-arrayexpress

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