RNA-seq
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina Genome Analyzer II, Illumina HiSeq 2000
ORGANISM(S): Homo sapiens
SUBMITTER: David Mole
PROVIDER: E-MTAB-1994 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Genome wide analysis RNA polymerase II (RNA Pol II) and histone marker H3K4me3 in hypoxia and normoxia using ChIP-seq. Breast cancer cell line (MCF-7) is cultured in normoxic condition (21% O2) and hypoxic condition (0.5%O2) for 16 hours. Immunoprecipitation of RNA Pol II and H3K4me3.
2014-02-10 | E-MTAB-1995 | biostudies-arrayexpress
Project description:Analysis of Huh-7 hepatocarcinoma cell line depleted of NDRG3 or HIF-1α under hypoxic condition. HIF-1α and NDRG3 have distinct functions in hypoxia responses. Results provide insight into molecular basis of HIF-independent signaling in the development and progression of hypoxic tumors Gene expression profiles of Huh-7 cells stably expressing NDRG3-shRNA or HIF-1α-shRNA under normoxia were compared to gene expression profiles of Huh-7 stable cells under hypoxia for 6, 12 and 24 hours.
2015-07-24 | E-GEOD-55212 | biostudies-arrayexpress
Project description:Analysis of Huh-7 hepatocarcinoma cell line depleted of NDRG3 or HIF-1α under hypoxic condition. HIF-1α and NDRG3 have distinct functions in hypoxia responses. Results provide insight into molecular basis of HIF-independent signaling in the development and progression of hypoxic tumors Gene expression profiles of Huh-7 cells stably expressing NDRG3-shRNA or HIF-1α-shRNA under normoxia were compared to gene expression profiles of Huh-7 stable cells under hypoxia for 3, 6, 12 and 24 hours.
2015-07-24 | E-GEOD-59729 | biostudies-arrayexpress
Project description:Purpose: We aimed to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression. Methods: microRNA sequencing data and gene expression microarray data were generated from MCF-7 cells submitted to an hypoxia timecourse (16h, 32h and 48h at 1% Oxygen). Data was integrated to 500 published high-stringency HIF binding sites identified in MCF-7 cells. Results: We identified 41 microRNAs significantly up- and 28 down- regulated, of which 38 mature and 20 star forms are reported in conjunction with hypoxia for the first time. HIF-1? and HIF-2? binding sites within 50kb distance of microRNA loci were found by integration of HIF ChIP-seq data, showing overall association between binding sites and up-regulation. Gene expression profiling analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts playing a role in microRNA processing were found regulated by hypoxia, of which two were HIF dependent. Conclusions: The data support the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level. HIF is involved at both levels, regulating the transcription of certain microRNAs and also the expression of key elements of the microRNA processing pathway. Gene expression profiles of MCF-7 exposed to hypoxia (1% Oxygen) for 16h (3 replicates), 32h (3 replicates) and 48h (3 replicates) and to normoxia (3 replicates) were generated using Illumina microarrays.
2014-02-13 | E-GEOD-47533 | biostudies-arrayexpress
Project description:Purpose: We aimed to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression. Methods: microRNA sequencing data and gene expression microarray data were generated from MCF-7 cells submitted to an hypoxia timecourse (16h, 32h and 48h at 1% Oxygen). Data was integrated to 500 published high-stringency HIF binding sites identified in MCF-7 cells. Results: We identified 41 microRNAs significantly up- and 28 down- regulated, of which 38 mature and 20 star forms are reported in conjunction with hypoxia for the first time. HIF-1M-NM-1 and HIF-2M-NM-1 binding sites within 50kb distance of microRNA loci were found by integration of HIF ChIP-seq data, showing overall association between binding sites and up-regulation. Gene expression profiling analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts playing a role in microRNA processing were found regulated by hypoxia, of which two were HIF dependent. Conclusions: The data support the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level. HIF is involved at both levels, regulating the transcription of certain microRNAs and also the expression of key elements of the microRNA processing pathway. microRNA-seq profiles of MCF-7 exposed to hypoxia (1% Oxygen) for 16h (2 replicates), 32h (2 replicates) and 48h (2 replicates) and to normoxia (2 replicates) were generated using Illumina sequencing platform.
2014-02-13 | E-GEOD-47602 | biostudies-arrayexpress
Project description:Purpose: We aimed to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression. Methods: microRNA sequencing data and gene expression microarray data were generated from MCF-7 cells submitted to an hypoxia timecourse (16h, 32h and 48h at 1% Oxygen). Data was integrated to 500 published high-stringency HIF binding sites identified in MCF-7 cells. Results: We identified 41 microRNAs significantly up- and 28 down- regulated, of which 38 mature and 20 star forms are reported in conjunction with hypoxia for the first time. HIF-1M-NM-1 and HIF-2M-NM-1 binding sites within 50kb distance of microRNA loci were found by integration of HIF ChIP-seq data, showing overall association between binding sites and up-regulation. Gene expression profiling analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts playing a role in microRNA processing were found regulated by hypoxia, of which two were HIF dependent. Conclusions: The data support the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level. HIF is involved at both levels, regulating the transcription of certain microRNAs and also the expression of key elements of the microRNA processing pathway. MicroRNA expression profiles of MCF-7 exposed to hypoxia (1% Oxygen) for 16h (2 replicates), 32h (3 replicates) and 48h (3 replicates) and to normoxia (3 replicates) were generated using Agilent miRNA microarrays. This data was used to validate the microRNA-seq data included in this study.
2014-02-13 | E-GEOD-47532 | biostudies-arrayexpress
Project description:DCs play a central role for the immune response against the mold Aspergillus fumigatus. Hypoxic microenvironments occur during infection with A. fumigatus. Hypoxia and signaling via hypoxia inducible factor 1α may modulate the response of DCs; however, the role in fungal infections is unclear. We used microarrays to determine the influence of hypoxia and HIF-1α signaling on the immune response of human DCs towards A. fumigatus. HIF-1α silenced or non-silenced, human monocyte-derived DCs were cultivated for 6 h in normoxia or hypoxia (1 % O2) without stimulation or stimulated with inactivated germ tubes of A. fumigatus. Three independent experiments with DCs derived from different blood donors were performed. RNA was extracted and hybridized on Affymetrix microarrays.
2015-11-01 | E-GEOD-60729 | biostudies-arrayexpress
Project description:Transcriptional profiling of H1299 non-small cell lung carcinoma cells transfected with either wt p53 or mut(175) p53 driven by the 5xHRE promoter (5 repeats of hypoxia-inducible factor response elements) and treated for 16 h with normoxia (21% O2) or hypoxia(<0.1% O2). 5xHRE promoter ensures that p53 expression is induced in hypoxic conditions only. Goal was to determine the transcriptional response of p53 in hypoxia and the 175 p53 mutant was used as a control as it is DNA-binding defective and transcription-incompetent mutant. Four-condition experiment: wt p53-transfected H1299 cells treated with normoxia, mut p53-transfected H1299 cells treated with normoxia, wt p53-transfected H1299 cells treated with hypoxia, mut p53-transfected H1299 cells treated with hypoxia. Biological replicates: 1 normoxic sample with wt p53, 1 normoxic sample with mut p53, 3 hypoxic samples with wt p53, 3 hypoxic samples with mut p53.
2014-01-08 | E-GEOD-53893 | biostudies-arrayexpress
Project description:Neuroendocrine (NE) carcinoma and NE differentiation (NED) of human prostate tumor are hallmarks of aggressive human prostate cancer. Here we reveal that HIF-1a cooperation with FoxA2, a transcription factor expressed in NE tissue, is required for determining NE phenotype. Reduced HIF-1a expression, as seen in the E3 ubiquitin ligase Siah2 mutant mice, converted NE tumors to atypical hyperplasia when crossed with the TRAMPTg mice. Significantly, HIF-1a cooperation with FoxA2 enables the trans-activation of select HRE-regulated genes such as Hes6, Plod2 and Jmjd1a, whose expression is notably higher in metastatic prostate adenocarcinomas. Our findings disclose the requirement for spatial and timely regulation of FoxA2 and HIF-1a for NE/NED in prostate tumors. 12 prostate tumor samples were analyzed during normoxia and hypoxia, with different FOX/HIF genotypes. The pivotal samples are represented as duplicates.
2010-07-13 | E-GEOD-18478 | biostudies-arrayexpress
Project description:Analysis of gene expression profile of B16-F10 murine melanoma cells exposed to hypoxic conditions (1% oxygen) or hypoxia mimicry (cobalt chloride) for 24 hours. Gene expression profiles were analyzed using MG-U74Av2 oligonucleotide microarrays. Data analysis revealed 2541 probesets (FDR<5%) for 1% oxygen experiment and 364 probesets (FDR<5%) for cobalt chloride, that showed differences in expression levels. Analysis of hypoxia-regulated genes (1% O2) by stringent Family-Wise Error Rate estimation indicated 454 significantly changed transcripts (p<0.05). The most upregulated genes were Lgals3, Selenbp1, Nppb (more than ten-fold increase). Both hypoxia and hypoxia-mimicry induced HIF-1 regulated genes. However, unsupervised analysis (Singular Value Decomposition) revealed distinct differences between gene expression induced by these two experimental conditions. We investigated transcriptional activity of B16-F10 murine melanoma cells cultured for 24h under hypoxic (nominal 1% oxygen; 9 experimental samples and 6 controls) and hypoxia-mimicking conditions (cobalt chloride, 100 M-NM-<M or 200 M-NM-<M, 2 samples each and 2 controls).
2011-11-11 | E-GEOD-33607 | biostudies-arrayexpress