Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of mpuse normal and SMAR1 overexpressing B16F10 cells

ABSTRACT: The present microarray studies the differential transcription levels of various genes upon overexpression of tumor suppressor protein SMAR1. The results will lead us to potential targets which are either up/downregulated by SMAR1. Experiment Overall Design: Agilent two-color experiment,Organism: Human ,Slides, Agilent’s Human Microarray G4110B with 22000 features, Labeling kit: Agilents Low input RNA linear amplification Kit Cat # 5184-3523, Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA

ORGANISM(S): Mus musculus

SUBMITTER: samit chattopadhyay

PROVIDER: E-GEOD-17795 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptional profiling of lung tissue of rat pretreated with cobalt in normoxic and hypoxic conditions and comapring with saline treated normoxic and hypoxic lung tissue in different time interval

Project description:The goal of the study was to examine the effect of hypoxic preconditioning with cobalt on global gene profiling in lung tissues. Agilent two-color experiment,Organism: Rat ,Slides, Agilentâs Whole Rat Genome Microarray 4x44k GPL4135 with 44000 features, Labeling kit: Agilents Low input RNA linear amplification Kit Cat # 5184-3523, Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA Rat lung tissue: cobalt + Hypoxia (0h, 6h, 12h, 24h, 48h) vs. Hypoxia (0h, 6h, 12h, 24, 48h)

2010-05-27 | E-GEOD-21239 | biostudies-arrayexpress

Transcription profiling of mouse embryos 1.5, 3 and 6 hr after maternal treatment with the teratogen sodium valproate

Project description:The antiepileptic drug valproic acid (vpa) is known teratogen giving neural tube defects (ntd:s). Administration of vpa to female NMRI on gestation day 8 induces a high incidence of ntd. In this study we investigate the time dependent gene expression changes induced in the embryo 1.5, 3 respectively 6 hr after maternal sodium valproate treatment.

2008-03-28 | E-MEXP-1062 | biostudies-arrayexpress

Aspp1 Preserves Hematopoietic Stem Cell Pool Integrity and Prevents Malignant Transformation

Project description:Quiescent hematopoietic stem cells (HSCs) are prone to mutagenesis, and accumulation of mutations can result in hematological malignancies. The mechanisms through which HSCs prevent such detrimental accumulation, however, are unclear. Here, we show that Aspp1 coordinates with p53 to maintain the genomic integrity of the HSC pool. Aspp1 is preferentially expressed in HSCs and restricts HSC pool size by attenuating self-renewal under steady state conditions. After genotoxic stress, Aspp1 promotes HSC cycling and induces p53-dependent apoptosis in cells with persistent DNA damage foci. Beyond these p53-dependent functions, Aspp1 attenuates HSC self-renewal and accumulation of DNA damage in p53-null HSCs. Consequently, concomitant loss of Aspp1 and p53 leads to the development of hematological malignancies, especially T-cell leukemia and lymphoma. Together, these data highlights coordination between Aspp1 and p53 in regulating HSC self-renewal and DNA damage tolerance, and suggest that HSCs possess specific mechanisms that prevent accumulation of mutations and malignant transformation. 8-week-old WT, Aspp1-/-, Mx1-Cre(+)p53flox/flox and Mx1-Cre(+)Aspp1-/-p53flox/flox mice were intraperitoneally administered with 400 μg pIpC five times every other day to obtain WT, Aspp1-/-, p53-/- and Aspp1-/-p53-/- bone marrow. 4 weeks after pIpC treatment, bone marrow lineage(-) Sca-1(+) cKit(+) cells were isolated. RNA was extracted and pooled from 3 independent mice per genotype. RNA samples were then amplified, labeled, and hybridized to independent arrays.

2015-05-20 | E-GEOD-69032 | biostudies-arrayexpress

CINCINNATA Controls Surface Curvature of Antirrhinum Leaf by Coordinated and Direct Activation of Cytokinin and Auxin Signaling

Project description:Mutations in the CINCINNATA gene in Antirrhinum and its orthologues in Arabidopsis cause negative surface curvature in leaves due to excess marginal growth. CIN-like genes code for TCP transcription factors and are expressed in a broad zone of a growing leaf somewhat distal to the proliferation zone. Although a few TCP targets are known, the role of CIN-like TCP genes in regulating leaf curvature has remained unclear. We have compared the global transcription profile of wild type and cincinnata mutant to identify its targets. By combining DNA-protein interaction, chromatin immunoprecipitation and RNA in situ hybridization, we show that CIN maintains surface flatness by regulating signaling or level of major plant hormones. CIN promotes cytokinin signaling directly and GA level indirectly, in accelerating maturity in leaf cells along the tip-to-base direction. In addition, CIN suppresses auxin signaling more at the margin than centre by establishing a margin-to-medial expression gradient of a homologue of the auxin suppressor IAA3. Our results uncover an underlying mechanism in a developing leaf that controls maturity of leaf and its surface curvature. Considering the conservation of CIN-like genes and their function in leaf morphogenesis in multiple plant species, it is likely that such mechanism is evolutionarily conserved. Two color Experiment, Organism: Arabidopsis thaliana and Antirrhinum. Arrays Used: 1. Agilent Arabidopsis thaliana Gene expression Microarray 22k (AMADID: 013324) 2. Agilent Custom Arabidopsis thaliana 4x44k Gene Expression (AMADID: 015226) 3. Agilent custom Antirrhinum 4x44k Gene expression (AMADID: 016341) designed by Genotypic Technology Private Limited.

2013-05-01 | E-GEOD-40621 | biostudies-arrayexpress

Comprehensive expression analysis of primary hepatocytes under four different culture conditions

Project description:Primary hepatocytes have been widely explored as cell sources for the study of in vitro drug metabolism and pharmacokinetics (DMPK). Aiming toward establishing an in vitro drug screening method, the current study illustrated a comprehensive increase in the DMPK-related gene expression of nanopillar (NP)-cultured 3D-spheroid. To examine the expressional changes in DMPK-related genes under four different conditions, namely, NP-, sandwich (SW)-, monolayer (ML)-cultured rat hepatocytes, and freshly isolated hepatocytes, genome-wide gene-expression analysis using a DNA microarray was performed. Among the DMPK-related genes, cytochrome P450, UDP-glucuronosyltransferase, and transporter genes were focused on. Principal component analysis showed that the global gene expression profile in sample from NP culture is closer to that from freshly isolated hepatocytes than that from SW culture. The expressions of almost all Cyp 1 to 3 and Ugt genes of NP-cultured 3-D spheroid were higher than those of ML and SW. The expression of Abcc2 gene whose translation product has a critical role in excretion of metabolized bile acids in hepatocyte to bile canaliculi was three times higher in NP than in ML. From these results, 3-D spheroid formed by the NP culture was suggested to possess higher ability of metabolism and excretion than conventional 2-D monolayer culture. The NP culture has a potential as an alternative culturing technique for evaluating metabolism and toxicity toward the development of new drugs. Gene expression in rat hepatocyte was measured under four different conditions, namely, Nanopillar (NP)-, sandwich (SW)-, monolayer (ML)-cultured rat hepatocytes, and freshly isolated hepatocytes. Three independent experiments were performed at 95 hours of post-seeding.

2015-06-25 | E-GEOD-38950 | biostudies-arrayexpress

Progression to Latent Infection Following Exposure to Mtb

Project description:These results were obtained in a controlled longitudinal experiment in which a group of rhesus macaques were exposed to a low dose of Mtb to study their progression to latent infection or active disease. Subsets of the animals were euthanized at scheduled time points, and granulomas taken from their lungs were assayed for gene expression. The clinical profiles associated with the animals following Mtb exposure revealed considerable variability, and we developed models for the disease trajectory for each subject using a Bayesian hierarchical B-spline approach. Disease severity estimates were derived from these fitted curves and included as covariates in linear models to identify genes significantly associated with disease progression. Our results demonstrate that the incorporation of clinical data increases the value of information extracted from the expression profiles and contributes to the identification of predictive biomarkers for TB susceptibility. Samples from 21 animals were included in this study. 18 rhesus macaques were exposed to Mtb and euthanisized according to a pre-defined schedule, and at least two granulomas were extracted from their lungs during necropsy. The remaining three animals were healthy controls and samples represent control lung tissues. The samples were arrayed using an extended loop design with animals grouped according to similar clinical profiles. Biological replication is provided in the form of at least two granuloma samples per animal.

2014-04-19 | E-GEOD-56919 | biostudies-arrayexpress

Gene expression of Epstein-Barr Virus (EBV) positive nodal peripheral T cell lymphoma, unspecified (PTCL-U)

Project description:EBV positive PTCL-U is a very rare but aggressive disease entity. To investigate gene expression profile, we performed gene expression analysis using two different types of microarray kits (Agilent chip 4x44K and 8x60K) We compared gene expression between in 3 EBV positive PTCL-Us and in 6 normal reactive lymph nodes.

2012-02-01 | E-GEOD-34143 | biostudies-arrayexpress

Gene expression profiles of the EBV-induced lymphomas against ‘normal’ human PBL

Project description:Peripheral blood lymphocytes (PBLs) were isolated from the fresh blood samples of six healthy donors and intraperitoneally grafted into SCID mice at 8~10 × 107 PBLs/mouse. PBLs from each donor were grafted into 3~4 SCID mice. EBV was isolated from the supernatant of B95-8 cells cultured in vitro under starvation conditions. EBV infection was not required for SCID mice that were grafted with PBLs from donors who were positive for EBV viral capsid antigen (VCA)-IgG and IgA. On the other hand, 0.4 mL of EBV suspension was intraperitoneally injected into SCID mice that were grafted with PBLs from donors who were VCA-IgA negative on day 3 post-grafting. All surviving mice were euthanized on day 135 post-PBL grafting. Total RNA was extracted from the six EBV-induced lymphomas (tumor group) and normal human lymphocytes (normal group) using TRIZOL reagent, and labelled as per the instructions of the Agilent Quick Amp Labeling Kit. First-strand cDNA was synthesized from purified total RNA (template) using the T7 promoter primer and Moloney murine leukemia virus reverse transcriptase, followed by the synthesis of the second-strand cDNA. Both cDNA strands were then synthesized into cRNA using transcription master mix and labelled with cyanine-3-cytidine-5'-triphosphate. Gene expression profiles of the normal and tumor groups were detected using Agilent whole genome microarray containing 41,000 known human gene transcripts. The microarrays were scanned with the Agilent Microarray Scanner and the raw data were recorded and normalized using Agilent Feature Extraction Software to calculate the signal fold change between the tumor and normal groups. A ≥2-fold change in gene expression, as determined by the t-test, was considered as up-regulated, and a ≤0.5-fold change in gene expression was considered as down-regulated.

2022-06-30 | E-MTAB-11857 | biostudies-arrayexpress

Elucidation of the expression profile of independent clones of mutant mtBALB and wild type control mtB6 murine cybrid cells

Project description:We generated murine fibroblast cybrid cell lines that have identical nuclear genomes and differ only in their mtDNA. We observed increased cellular proliferation and resistance to apoptosis in the mtBALB compared to the mtB6 cybrid cells, phenotypes seen in malignant cells. Based on these observations we investigated whether these phenotypic differences could be caused by a unique spectrum of nuclear gene expression alterations induced by the mtDNA changes. Microarray analysis (Agilent, 44K mouse whole genome chip) was conducted in order to elucidate the expression profile of three independent clones of mtBALB and mtB6 cybrid cells. Two-condition experiment, mtB6 vs. mtBALB cells. Biological replicates: 4 control replicates, 4 mutant replicates.

2012-06-25 | E-GEOD-21855 | biostudies-arrayexpress

Genome-wide gene expression comparison (primary central nervous system lymphoma (PCNSL) vs normal lymph node)

Project description:A genome-wide gene expression comparison between primary central nervous system lymphoma (PCNSL) and normal lymph node was performed to identify a differential exprssion and specific pathway. Experiment design: 7 PCNSL and 7 normal lymph node tissues were used for comparison.

2010-11-13 | E-GEOD-25297 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data