Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of gene expresson between larger sized tetraploid and smaller sized diploid HCA2

ABSTRACT: In order to determine the factors that regulate senescence induction, we tried to identfy genes that are predominantly expressed in large sized senescent cells with tetraploid DNA. We sorted large or small sized HCA2 cells treated wth IR (10Gy) according to size and structure (FSC and SSC) by FACScan and analyzed global gene expression patterns.

ORGANISM(S): Homo sapiens

SUBMITTER: Yoshikazu Johmura

PROVIDER: E-GEOD-69116 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparison of gene expresson between larger sized tetraploid and smaller sized diploid HCA2

Project description:In order to determine the factors that regulate senescence induction, we tried to identfy genes that are predominantly expressed in large sized senescent cells with tetraploid DNA.

2015-05-22 | GSE69116 | GEO

Transcription profiling of human dermal fibroblasts treated with 10Gy gamma radiation and remain in culture for 6h at 37?C

Project description:Cells were treated with 10Gy gamma radiation and remain in culture for 6h at 37°C with 5 % CO2 and 95 % humidity.

2007-04-25 | E-RZPD-21 | biostudies-arrayexpress

DNA damage-induced differentiation of NSC

Project description:Murine ES-derived neural stem cells (NSC) were not irradiated (ctrl) or irradiated with 10Gy and cultured for 7 days (irr). The goal was to study the gene expression changes in NSC at d7 after irradiation. Total RNA was extracted from 4 ctrl and 4 irr samples (biological quadruplicates).

2013-07-25 | E-GEOD-38031 | biostudies-arrayexpress

Transcription profiling of mouse PKBalpha embryonic fibroblast irradiation response

Project description:MEF proficient or deficient in PKBalpha, or PKBalpha knockout MEF where PKBalpha expression was reconstituted by stable transfection were subjected to 10Gy gamma-IR treatment. 4 or 24 hours after treatment, gene expression changes were analyzed. Experiment Overall Design: three biological replicates were included in the experiment for each condition analyzed. overall, 27 samples were included in the study. the reference samples were untreated MEF of each respective genotype.

2008-06-17 | E-GEOD-9146 | biostudies-arrayexpress

Gene expression levels in immortalized B cells from 95 unrelated CEPH-Utah individuals treated with 10Gy of ionizing radiation

Project description:We used microarrays to examine gene expression levels from 95 unrelated CEPH-Utah individuals 0, 2 or 6 hours after treatment with 10Gy of ionizing radiation. We measured gene expression levels in immortalized B cells from 95 unrelated CEPH-Utah individuals. Each individual was treated with 10Gy of ionizing radiation and expression was measured 0, 2 and 6 hour after treatment.

2013-03-28 | E-GEOD-36910 | biostudies-arrayexpress

Phosphoproteomic profiling of the DNA damage response in MCF10A and human PBMC cells by SILAC labeling and 1D and 2D-LC-MS/MS

Project description:The DNA-damage response (DDR) is a critical network for maintaining genomic integrity, and mutations in the DDR are among the most frequently identified in tumors. Phosphorylation is a key signaling event in the DDR network. We sought to design high throughput, mass spectrometry based assays to monitor phosphopeptides in the DDR network for biological experiments and pharmacodynamics studies. These assays require an enrichment step, which can be done using antibodies. Developing antibodies de novo for phosphopeptide enrichment is costly and time-consuming, so we assessed the feasibility of immobilized-metal affinity chromatography (IMAC) enrichment coupled with multiple reaction monitoring-mass spectrometry (MRM-MS) for precise measurement of large numbers of phosphopeptides in the DDR network. Towards this goal, we evaluate the ability of the approach to reproducibly measure the endogenous phosphorylation levels of proteins associated with the DDR. Reproducibly detectable phosphopeptide targets for MRM-based assay development were empirically identified from LC-MS/MS analyses of SILAC-labeled MCF10A human breast epithelial cells exposed or mock-exposed to DNA damage. Samples were treated in triplicate with either ionizing radiation (IR) or methyl methanesulfonate (MMS) as the DNA-damaging agent. SILAC-labeled cells were prepared in two separate (label swap) experiments. First, treated cell lines were grown in heavy SILAC medium and untreated in light, and second, this labeling scheme was reversed. Untreated and treated cells were mixed at a 1:1 ratio by protein mass. To identify phosphopeptides at levels observable by MRM in an approach amenable to moderate throughput, a single step IMAC enrichment was developed for rapid processing of whole cell lysate.

2015-12-01 | PXD002363 | Pride

RNAseq of human epithelial lung carcinoma cell line A549 exposed to ceria, silver or zinc ions, micron-sized particles or nanoparticles

Project description:The toxicity of silver and zinc oxide nanoparticles is hypothesised to be mediated by dissolved metal ions and cerium dioxide nanoparticles (CeO2 NPs) are hypothesised to induce toxicity specifically by oxidative stress dependant on their surface redox state. To test these hypotheses, RNAseq was applied to characterise the molecular responses of cells to metal nanoparticle and metal ion exposures. The human epithelial lung carcinoma cell line A549 was exposed to different CeO2 NPs with different surface charges, micron-sized and nano-sized silver particles and silver ions, micron-sized and nano-sized zinc oxide particles and zinc ions, or control conditions, for 1 hour, 6 hours and 24 hours. Concentrations were the lower of either EC20 or 128 micrograms/mL. Transcriptional responses were characterised by RNAseq transcriptomics using an Illumina HiSeq2500 .

2018-02-01 | E-MTAB-5734 | biostudies-arrayexpress

Senescent and myofibroblastic cancer-associated fibroblasts share a contractile phenotype regulated by NOX4 generation of reactive oxygen species in the tumour microenvironment

Project description:Cancer associated fibroblasts characterized by an myofibroblastic phenotype play a major role in the tumour microenvironment, being associated with poor prognosis. We found that this cell population is made in part by senescent fibroblasts in vivo. As senescent fibroblasts and myofibroblasts have been shown to share similar tumour promoting functions in vitro we compared the transcriptosomes of these two fibroblast types and performed RNA-seq of human foetal foreskin fibroblasts 2 (HFFF2) treated with 2ng/ml TGF-beta-1 to induce myofibroblast differentiation or 10Gy gamma irradiation to induce senescence. We isolated RNA 7 days upon this treatments changing the medium 3 days before the RNA extraction. A series of SAM alignment files (named after the sample names, for simplicity) are available under http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3101/files/ .

2017-06-01 | E-MTAB-3101 | biostudies-arrayexpress

Identification of intermediate-sized non-coding RNAs involved in the UV-induced DNA damage response in C. elegans

Project description:We utilized high-throughput RNA-seq to uncover the intermediate-sized noncoding RNAs invovled in UV-DNA Damage Responses in C. elegans. 450 novel transfrags were discovered, some of which show dramatic expression change between the UV irradiation and control. This study should lead to a better understanding of the role of is-ncRNAs invovled in UV-DDR. Examination of intermediate-sized transcripts (70-500nt) in L4 larvae of C. elegans strains, including wild-type (N2), UV-irradiated (N2-UV100J/m2) and NER-deficient mutant (xpa-1) strains.

2012-05-01 | E-GEOD-37063 | biostudies-arrayexpress

Transcription profiling of human lung epithelial cells (A549) treated with nano- and micro-sized silica and carbon particles to study toxic effects related to size and chemical origin

Project description:To screen for novel toxicological endpoints of nano-particles, we conducted an in vitro expression profiling study using human lung epithelial cells (A549). To identify effects that are specific to size or chemical origin, we compared gene expression of A549 cells treated with nano-sized and micro-sized particulates of two chemical origins (carbon and silica) to the control (untreated) cells.

2009-07-10 | E-TABM-679 | 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