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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide analysis of gene expression perturbed by reptin shRNA in MCF7 subjected to normoxic and hypoxic conditions

ABSTRACT: In order to investigate the role of reptin methylation on the expression of hypoxia-responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shRNA) or reptin shRNA (shreptin) in normoxic and hypoxic conditions. MCF7 cells were transiently transfected with either non-specific shRNA or reptin shRNA in replicates. Cells were grown for 24 hours before being exposed to either normoxic (21% oxygen) or hypoxic (1% oxygen) conditions for 18 hours. Cells were then lysed and RNA was isolated.

ORGANISM(S): Homo sapiens

SUBMITTER: Minhyung Kim

PROVIDER: E-GEOD-15530 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Negative regulation of hypoxic responses via induced Reptin methylation.

Lee Jason S JS Kim Yunho Y Kim Ik Soo IS Kim Bogyou B Choi Hee June HJ Lee Ji Min JM Shin Hi-Jai R HJ Kim Jung Hwa JH Kim Ji-Young JY Seo Sang-Beom SB Lee Ho H Binda Olivier O Gozani Or O Semenza Gregg L GL Kim Minhyung M Kim Keun Il KI Hwang Daehee D Baek Sung Hee SH

Molecular cell 20100701 1

Lysine methylation within histones is crucial for transcriptional regulation and thus links chromatin states to biological outcomes. Although recent studies have extended lysine methylation to nonhistone proteins, underlying molecular mechanisms such as the upstream signaling cascade that induces lysine methylation and downstream target genes modulated by this modification have not been elucidated. Here, we show that Reptin, a chromatin-remodeling factor, is methylated at lysine 67 in hypoxic co ...[more]

PMID: 20603076

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Genome-wide analysis of gene expression perturbed by Pontin shRNA in MCF7 subjected to normoxic and hypoxic conditions

Project description:In order to investigate the role of Pontin methylation on the expression of hypoxia responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shNS) or Pontin shRNA(shPontin) in normoxic and hypoxic conditions. MCF7 cells were transiently transfected with either non-specific shRNA or Pontin shRNA in replicates. Cells were grown for 24 hours before being exposed to either normoxic (21% Oxygen) or hypoxic condition (1% oxygen) for 6,9 hours. Cells were then lysed and RNA isolated.

2011-12-02 | E-GEOD-27813 | biostudies-arrayexpress

Genome-wide analysis of gene expression perturbed by reptin shRNA in MCF7 subjected to normoxic and hypoxic conditions

Project description:In order to investigate the role of reptin methylation on the expression of hypoxia-responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shRNA) or reptin shRNA (shreptin) in normoxic and hypoxic conditions.

2010-07-13 | GSE15530 | GEO

Genome-wide analysis of gene expression perturbed by Pontin shRNA in MCF7 subjected to normoxic and hypoxic conditions

2011-12-02 | GSE27813 | GEO

Characterization of the transcriptional response to hypoxia in MDA-MB-231-shCAIX, MCF7-shCAIX and the respective control cells grown as multicellular spheroids under hypoxic or normoxic conditions

Project description:To interrogate the hypoxia response pathways affected by the depletion of CAIX in BC cells, we performed gene expression profiling using SurePrint G3 Human Gene Expression 60K microarrays in MDA-MB-231-shCAIX, MCF7-shCAIX and the respective control cells grown as multicellular spheroids under hypoxic or normoxic conditions. The human breast cancer cell lines MDA-MB-231 and MCF7 were purchased from the European Collection of Cell Cultures (ECACC, UK) and maintained as recommended by the manufacturer. To generate stable CAIX silenced cells, cell lines were transfected with a pool of three plasmids each encoding CAIX-specific shRNA (1 µg) and a negative control (NC) plasmids encoding scrambled shRNAs (1 µg) (Santa Cruz Biotechnology, TX, USA) using shRNA transfection medium and shRNA transfection reagent (Santa Cruz Biotechnology, USA) according to the manufacturers’ protocol. For selection of stably transfected cells, puromycin dihydrochloride (Santa Cruz Biotechnology, USA) was added to medium 48 h post-transfection (6 µg/ml for MCF7, 2 µg/ml for MDA-MB-231 cells). The transfected cells were plated at density 2e+3 cells per ml of serum-free DMEM/F12 medium supplemented with EGF (20ng/ml, R&D Systems, #236-EG-200), bFGF (10ng/ml, SantaCruz, #sc-4573), hydrocortisone (50 ng/ml, Sigma-Aldrich, #H0135-1MG) and 1B27 (Invitrogen, #17504001) and grown as multicellular spheroids for 5 days. To establish hypoxic conditions, the cells were cultured at 1% oxygen, 94% N2 and 5% CO2 at 37oC using humidified multi-gas incubator (Sanyo, Sanyo Electric Co.,Ltd.) for 48 hours. The normoxic control cells were incubated at 37oC with 5% CO2 in a humidified incubator (Panasonic, Panasonic Healthcare Co., Ltd.). The efficiency of CAIX silencing was assessed by qRT-PCR and immunofluorescence before the experiments.

2018-01-01 | E-MTAB-5512 | biostudies-arrayexpress

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2020-12-19 | E-MTAB-9452 | biostudies-arrayexpress

Transcription profiling of human neuroblastoma cell lines grown under normoxic and hypoxic conditions

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2009-10-10 | E-GEOD-17714 | biostudies-arrayexpress

Transcriptional response of Candida parapsilosis in low oxygen (hypoxic) conditions in SD media

Project description:Whole genome microarray was used to compare the transcriptional profile of C. parapsilosis growing in normoxic (21% oxygen) and hypoxic (1% oxygen) conditions. RNA was isolated from cells grown in SD media at 37Â°C for 3 h in atmosphere oxygen of 1% oxygen, and labeled with Cy5 or Cy3. Six independent biological replicates were compared. 4 out of 6 hypoxic samples were labeled with Cy5, and 2 were labeled with Cy3.

2010-05-06 | E-GEOD-13722 | biostudies-arrayexpress

Genome-wide maps of DNase I sensitivity in normoxic and hypoxic cells

Project description:We report genome-wide maps of DNase I sensitivity in normoxic and hypoxic cells to provide information on changes in chromatin status in response to oxygen availability.

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Transcription profiling by array of heart tissue from rats kept in normoxic or hypoxic conditions

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2010-08-18 | E-MEXP-2863 | biostudies-arrayexpress

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Project description:TECs cultured in normoxic conditions, TECs cultured in hypoxic conditions and TECs cultured in hypoxic treated with EPc derived microvesicles

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