Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human umbilical vein endothelial cells to investigate the effects of Serum Amyloid A, time series

ABSTRACT: This study attemps to study the global effects of Serum Amyloid A (SAA) on human endothelial gene expression profile in different time points. Experiment Overall Design: HUVECs were cultured to confluence in 6-well plates and stimulated with 20 Î¼g/ml of SAA (PeproTech) for 0, 4, 24 and 48 h. To determine the cellular transcript profile in Control (0h) and 3 different SAA groups (S4h, S24h and S48h), the relative abundance of mRNAs in SAA groups were compared with Control by use of Human Genome U133 Plus 2.0 Array (HG-U133 Plus 2.0, Affymetrix)). Each group had 2 individual samples. . In order to obtain the 3 group comparison datasets (S4h/C, S24h/C and S48h/C), expression patterns for each individual SAA sample (4h, 24h and 48h) were compared to each individual control sample. Hence, each group comparison has 4 individual sample comparisons. The robust increased or decreased cut-off was use the Affymetrix recommending "1" or "-1" of the signal log ratio. . If the gene is robust âincreasedâ or âdecreasedâ in 4 individual sample comparisons of the total 4 comparisons, it was selected as the final robust changed in group comparison. Each gene we were interested, real time PCR was carried out to validate the microarray results.

ORGANISM(S): Homo sapiens

SUBMITTER: yulan zhao

PROVIDER: E-GEOD-6241 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Gene expression profiling is an important tool in the development of medical countermeasures against chemical warfare agents (CWAs). Non-human primates (NHPs), specifically the rhesus macaque (Macaca mulatta), the cynomologus macaque (Macaca fascicularis) and the African green monkey (Chlorocebus aethiops), are vital models in the development of CWA prophylactics, therapeutics, and diagnostics. However, gene expression profiling of these NHPs is complicated by the fact their genomes are not completely sequenced, and that no commercially available oligonucleotide microarrays (genechips) exist. We, therefore, sought to determine whether gene expression profiling of NHPs could be performed using human genechips. Whole blood RNA was isolated from each species and used to generate genechip probes. Hybridization of the NHP samples to human genechips (Affymetrix Human U133 Plus 2.0) resulted in comparable numbers of transcripts detected compared with human samples. Statistical analysis revealed intraspecies reproducibility of genechip quality control metrics; interspecies comparison between NHPs and humans showed little significant difference in the quality and reproducibility of data generated using human genechips. Expression profiles of each species were compared using principal component analysis (PCA) and hierarchical clustering to determine the similarity of the expression profiles within and across the species. The cynomologus group showed the least intraspecies variability, while the human group showed the greatest intraspecies variability. Intraspecies comparison of the expression profiles identified probesets that were reproducibly detected within each species. Each NHP species was found to be dissimilar to humans; the cynomologus group was the most dissimilar. Interspecies comparison of the expression profiles revealed probesets that were reproducibly detected in all species examined. These results show that human genechips can be used for expression profiling of NHP samples and provide a foundation for the development of tools for comparing human and NHP gene expression profiles. Keywords = human Keywords = homo sapien Keywords = blood Keywords = rhesus macaque Keywords = cynomologus macaque Keywords = African green monkey Keywords: parallel sample

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Transcription profiling of human umbilical vein endothelial cells to investigate the effects of Serum Amyloid A, time series

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