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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Microarray analysis of MCF7 cells treated with NSC 59687 (Oxyphenisatin Acetate)

ABSTRACT: NSC 59687 (oxyphenisatin acetate) is a novel anti-cancer agent with selectivity for breast and ovarian cell lines To elucidate the transcripts differentially regulated following treatment with Oxyphenisatin acetate (NSC 59687) MCF7 cells were treated with 10 microM NSC 59687 for 24 hours followed by RNA extraction, cDNA synthesis and microarray analysis using Affymetrix huU133 plus 2.0 arrays

ORGANISM(S): Homo sapiens

SUBMITTER: Luke Stockwin

PROVIDER: E-GEOD-45046 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Microarray analysis of MCF7 cells treated with NSC 59687 (Oxyphenisatin Acetate)

Project description:NSC 59687 (oxyphenisatin acetate) is a novel anti-cancer agent with selectivity for breast and ovarian cell lines To elucidate the transcripts differentially regulated following treatment with Oxyphenisatin acetate (NSC 59687)

2013-03-13 | GSE45046 | GEO

Compare gene expression profiles of mouse iNSC, WT-NSC, and MEF

Project description:The iNSC cells are two clones generated from the same MEF line. Therefore, we conducted one analysis that compared the two clonal lines and a separate analysis that compared iNSC vs. NSC, iNSC vs. MEF, and NSC vs. MEF. Both were single factor ANOVAs, the first compared two groups (the iNSC lines) and the second had three groups. For the second analysis, we then used linear contrasts to extract the information about differences between all pairs (e.g. iNSC vs. NSC). Looking at the iNSC lines, the correlations between samples from different clonal lines are as high as the correlations between samples from within a clonal line. Given this, we think that the analysis that combines all 6 of them to compare against the other cell types is appropriate. Array Platform: Affymetrix Mouse Gene 1.0 ST Samples: A total of 12 arrays array# filename genotype 1 01.iNSC1.1.CEL iNSC 2 02.iNSC1.2.CEL iNSC 3 03.iNSC1.3.CEL iNSC 4 04.iNSC2.1.CEL iNSC 5 05.iNSC2.2.CEL iNSC 6 06.iNSC2.3.CEL iNSC 7 07.WT.NSC.1.CEL NSC 8 08.WT.NSC.2.CEL NSC 9 09.WT.NSC.3.CEL NSC 10 10.WT.MEFs.1.CEL MEF 11 11.WT.MEFs.3.CEL MEF 12 12.WT.MEFs.5.CEL MEF

2012-06-06 | E-GEOD-37859 | biostudies-arrayexpress

Gene expression analysis of H9 hESC derived neuron stem cells (NSC) harboring pathogenic LRRK2 (G2019S) mutation

Project description:Genetic mutations on leucine-rich repeat kinase 2 (LRRK2) have been associated with an increased risk of Parkinson's disease. The Gly2019Ser (G2019S) mutation on LRRK2 gene is a relatively common cause of familial Parkinson's disease in Caucasian population. In this study, we generated H9 hESC harboring LRRK2 (G2019S) mutation by gene knockin. Wildtype and LRRK2 mutant hESC were differentiated into NSC using a chemically defined protocol. LRRK2 mutant NSC were treated with or without the LRRK2 kinase specific inhibitor (LRRK2-IN-1). Global gene expression analysis was performed to assess the overall similarity of gene expression profiles among three NSC groups (wildtype; LRRK2 mutant; LRRK2 mutant with inhibitor treatment).

2012-10-17 | E-GEOD-36321 | biostudies-arrayexpress

Expression profile of Ceacam1 downstream genes in NSC and NSCL61

Project description:To identify Ceacam1 downstream factors, we compared gene expressions between NSCs and Ceacam1L-expressing NSC and between NSCL61 and Ceacam1shRNA-expressing NSCL61. We established Ceacam1L-expressing NSC and Ceacam1shRNA-expressing NSCL61s. We think that genes, which are differently expressed between NSC and Ceacam1L-NSC, and between NSCL61 and Ceacam1shRNA-NSCL61, are the Ceacam1 downstream factors.

2015-11-04 | E-GEOD-70023 | biostudies-arrayexpress

Evaluating cross-hybridization of murine cDNA to the Affymetrix Human Genome U133 Plus 2.0 chipset

Project description:Transcriptomic studies of human tumor xenografts are complicated by the presence of murine cellular mRNA. As such, it is useful to know the extent to which mouse mRNA cross-hybridizes to any given array platform. In this study, murine cDNA samples from diverse sources were hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays. In this regard it is possible to identify specific probes that are potential targets of cross-species interference. Array data was generated for 5 different mouse cDNAs and 5 different human cDNAs hybridized to human Affymetrix U133 Plus 2 arrays [3 replicates for each biological sample]. Samples included A) mouse and B) human universal RNA (Strategene, La Jolla, CA), C) B16F10 murine melanoma tumor and D) skin from same model [C57BL/6 mice] E) COLON-26 murine tumor xenograft and F) skin from same model [Balb/C mice] G) NCI-H522 human lung carcinoma xenograft and H) skin from same model (nude mice) I) LOX-IMVI human melanoma xenograft and J) skin from same model (nude mice).

2013-07-31 | E-GEOD-49353 | biostudies-arrayexpress

Gene expression analysis of H9 hESC derived cardiomyocytes (CM) and neuron stem cells (NSC)

Project description:In this study, we generated wildtype H9 hESC derived cardiomyocytes (CM) and neural stem cells (NSC) by in vitro differentiation. Global gene expression profiles were compared among undifferentiated H9 hESC and the derived CM and NSC. Comparison of global gene expression profiles of undifferentiated H9 hESC and the derived CM and NSC populations.

2013-08-31 | E-GEOD-48257 | biostudies-arrayexpress

Transcription profiling of human MCF7 cells treated with ARC (NSC 188491)

Project description:ARC (NSC 188491, SMA-491), 4-amino-6-hydrazino-7-beta-d-ribofuranosyl-7H-pyrrolo-(2,3-d)-pyrimidine-5-carboxamide, is a nucleoside analog with profound in vitro anti-cancer activity. First identified in a high-throughput screen for inhibitors of p21 mRNA expression, subsequent experiments showed that ARC also repressed expression of hdm2 and survivin, leading to its classification as a global inhibitor of transcription 1. The following Hu U133 plus 2.0 arrays represent single time point (24 hour) gene expression analysis of transcripts altered by ARC treatment. Arrays for the other compounds (sangivamycin and doxorubicin) are included as comparators. Experiment Overall Design: MCF7 cells treated with ARC, Sangivamycin or Doxorubicin for 24 hours.

2008-11-15 | E-GEOD-13477 | biostudies-arrayexpress

Microarray analysis of xenograft models in use at the Developmental Therapeutics Program of the National Cancer Institute (DTP-NCI)

Project description:Xenograft models remain a cornerstone technology in the development of anti-cancer agents. The ability of immunocompromised rodents to support the growth of human tumors provides an invaluable transition between in vitro testing and clinical trials. Therefore, approaches to improve model selection are required. In this study, cDNA microarray data was generated for a collection of xenograft models at in vivo passages 1, 4 and 10 (P1, P4 and P10) along with originating cell lines (P0). These data can be mined to determine transcript expression 1) relative to other models 2) with successive in vivo passage and 3) during the in vitro (P0) to in vivo (P1) transition. For originating cell lines (P0) and xenograft fragments at P1, P4 and P10, RNA was isolated, cDNA transcribed and hybridized to Affymetrix HG-U133 Plus 2.0 arrays. P0 samples have 2-3 replicates, whereas P1, P4 and P10 samples have 5 replicates. This dataset comprises a total of 823 array files.

2013-07-01 | E-GEOD-48433 | biostudies-arrayexpress

Global gene expression analysis of human iPSC-derived Neural Stem Cells (NSC) from LCA patients and unaffected persons

Project description:Our purpose was to investigate genes and molecular mechanisms involved in patients with Leber congenital amaurosis (LCA). Fibroblasts from two unrelated clinically-identified patients (Coriell) were reprogrammed to pluripotency by retroviral transduction. These human induced Pluripotent Stem Cells (hiPSCs) were differentiated into neural stem cells (NSC) that mimicked the neural tube stage and retinal pigmented epithelial (RPE) cells that could be targeted by the disease. A genome wide transcriptome analysis was performed with Affymetrix Exon Array GeneChipM-BM-., comparing LCA-hiPSCs derivatives to controls. The aim was to identify differentially expressed genes which may be associated with early developmental defect before the establishment of mature retinal circuitry. We analyzed iPSC-derived neural stem cells from LCA patient's fibroblast (n=2) and iPSC-derived neural stem cells from healthy people fibroblast (n=2). A total of 21 samples were analyzed : 9 NSC derived from iPSC LCA and 12 NSC derived from wild-type iPSC.

2015-01-21 | E-GEOD-43924 | biostudies-arrayexpress

NSC-derived exosomes enhance therapeutic effects of NSC transplantation on cerebral ischemia in mice

Project description:Transplantation of neural stem cells (NSCs) has been proved to promote functional rehabilitation of brain lesions including ischemic stroke. However, the therapeutic effects of NSC transplantation is limited by the low survival and differentiation rates of NSCs due to the harsh environment in the brain after ischemic stroke. Here, we employed NSCs derived from human induced pluripotent stem cells (iPSCs) together with exosomes extracted from NSCs to treat cerebral ischemia induced by middle cerebral artery occlusion/reperfusion (MCAO/R) in mice. The results showed that NSC-derived exosomes significantly reduced the inflammatory response, alleviated oxidative stress after NSC transplantation, and facilitated NSCs differentiation in vivo. The combination of NSCs with exosomes ameliorated the injury of brain tissue including cerebral infarct, neuronal death and glial scarring, and promoted the motor function recovery. To explore the underlying mechanisms, we analyzed the miRNA profiles of NSC-derived exosomes and the potential downstream genes. Our study provided the rationale for the clinical application of NSC-derived exosomes as a supportive adjuvant for NSC transplantation after stroke.

2023-04-26 | GSE217074 | GEO

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