Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comparison of hypoxia (4 % O2) cultured human embryonic stem cells (hESCs) to normoxia (21 % O2) cultured

ABSTRACT: We compared the transcriptome at gene expression level in hypoxic and normoxic conditions. The transcriptome of cells cultured at three different timepoints, 2h, 24 h and 7 days with three different cell lines in normoxia and hypoxia was compared 18 samples total, 3 replicates in each conditions, 2h, 24 h and 7day timepoints in hypoxia and normoxia

ORGANISM(S): Homo sapiens

SUBMITTER: Elisa Närvä

PROVIDER: E-GEOD-35819 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Continuous hypoxic culturing of human embryonic stem cells enhances SSEA-3 and MYC levels.

Närvä Elisa E Pursiheimo Juha-Pekka JP Laiho Asta A Rahkonen Nelly N Emani Maheswara Reddy MR Viitala Miro M Laurila Kirsti K Sahla Roosa R Lund Riikka R Lähdesmäki Harri H Jaakkola Panu P Lahesmaa Riitta R

PloS one 20131113 11

Low oxygen tension (hypoxia) contributes critically to pluripotency of human embryonic stem cells (hESCs) by preventing spontaneous differentiation and supporting self-renewal. However, it is not well understood how hESCs respond to reduced oxygen availability and what are the molecular mechanisms maintaining pluripotency in these conditions. In this study we characterized the transcriptional and molecular responses of three hESC lines (H9, HS401 and HS360) on short (2 hours), intermediate (24 h ...[more]

PMID: 24236059

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Project description:Background: Lung cancer has the highest mortality rate of all the cancers in the world and asbestos-related lung cancer is one of the leading occupational cancers. The identification of the asbestos-related molecular changes has been a topic of major research interest over the years. The aim of the current study was to identify novel asbestos-related molecular correlates by integrating miRNA expression profiling with previously obtained microarray data (aCGH and mRNA expression) from the same patient material. Results: Twelve novel asbestos-related miRNAs (over-expressed: miR-148b, miR-374a, miR-24-1*, Let-7d, Let-7e, miR-199b-5p, miR-331-3p and under-expressed: miR-939, miR-671-5p, miR-605, miR-1224-5p, miR-202) which inversely correlated with target genes (e.g. GADD45A, LTBP1, FOSB, NCALD, CACNA2D2, MTSS1, EPB41L3) were identified. In addition, several known and new lung cancer-associated miRNAs were identified. DNA copy number alterations were also correlated with the deregulation of four miRNAs in lung cancer. The importance of integrated analysis was highlighted by the interesting finding of linking of the over-expression of well known squamous cell carcinoma-associated miR-205 with the down-regulation of the gene DOK4. Conclusions: Novel deregulated miRNAs and inversely correlating expression of target genes associated with lung cancer etiology and histology were identified. In addition, DNA copy number alterations correlated with the deregulation of some of the miRNAs. The results of the current study could have potential diagnostic implications, but require further investigation. Methods: The patient material used in the study consisted of 26 tumour and normal lung tissue from highly asbestos-exposed (13 samples) and non-exposed (13 samples) patients. Control lung tissue samples were obtained from 7 patients without cancer as well as from a commercial lung tissue RNA. Data analysis on miRNA expression and integration of miRNA and mRNA data were performed using Chipster (http://chipster.csc.fi/). In addition, miRNA and aCGH data were integrated in a separate analysis. *** This submission represents the microRNA component of the study

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Dataset Information

Comparison of hypoxia (4 % O2) cultured human embryonic stem cells (hESCs) to normoxia (21 % O2) cultured

Publications

Continuous hypoxic culturing of human embryonic stem cells enhances SSEA-3 and MYC levels.

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