Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression in response to low-intensity pulsed ultrasound treatment of bone marrow cells under osteogenic conditions in vitro

ABSTRACT: We performed a comprehensive analysis of gene expression changes following low-intensity pulsed ultrasound (LIPUS) treatment of cultured bone marrow cells under bone formation conditions, using cDNA microarray analysis Bone marrow cells were obtained from the femora of rats and were suspended in an osteogenic medium to make a cell culture. After cultures were established, test cultures were exposed to LIPUS via the base of the cell culture plates for 15 min/day on days 3–9 (LIPUS group). Control cultures (without LIPUS exposure) were otherwise treated identically to the LIPUS group. On day 10, total RNA was extracted from both sets of cultures and hybridized to microarray slides, the data sets were analysed. Markers for differentiated osteoblasts and osteocytes, as well as collagen-related genes, cell adhesion factors were up-regulated in LIPUS group on day 10. Gene expression in response to LIPUS treatment of bone marrow cells were measured on day 10 after cultures were established. Experiments were performed at each conditions (LIPUS or Control).

ORGANISM(S): Rattus norvegicus

SUBMITTER: Daisuke Yamaguchi

PROVIDER: E-GEOD-70662 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:To compare tumor associated macrophage (TAM) from naïve and sepsis surviving mice we have employed Agilent microarrays slides with almost 60,000 genes (39,430 mRNA and 16,251 long non coding RNAs). Other experiments we conducted demonstrated TAM accumulation was increased in post-sepsis subjects. For this reason, we asked if TAM from post-sepsis mice could also exhibit a different gene expression profile. Sepsis was induced by cecal and ligation puncture. Naïve mice were used as control group. All animals were treated with ertapenem (20 mg/kg, i.p., 6 hours after surgery, and then each 12 hours for 3 days). B16-F10 melanoma (30,000 cells) were injected subcutaneously at day 14 after sepsis induction. Fourteen days after tumor inoculation, animals were killed and tumors were harvested and digested (collagenase and DNAse). TAM was isolated by a Percoll gradient (70/30) followed by a 1-hour adhesion protocol, reaching a purity of ~75%. For comparative reasons, we assessed TAM from post-sepsis (n = 4), TAM from naïve mice (n = 4), bone marrow derived macrophage from naïve (n = 4) and from post-sepsis (n = 4), M1-polarized macrophage (n = 4) and M2-polarized macrophage (n = 4). We found only minor gene expression differences between TAM from naïve and from post-sepsis mice (61 genes were up-regulated and 98 genes were down-regulated, fold-change > 0.58 or < -0.58, and p < 0.01). We found genes related to leukocyte activation were down-regulated in TAM from post-sepsis mice (e.g. Ccr7, Cd86, H2-Ab1), as well as genes related to antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (H2-DMb1, Cd74, H2-Eb1, H2-Ob). A gene related to M2 polarization was up-regulated (Marco). Also, we found a down-regulation of Nfkbid in post-sepsis-derived TAM. This led us to hypothesize TAM from post-sepsis mice exhibit a more M2-like phenotype, which may in part contribute to post-sepsis tumor expansion. Three independent experiments were conducted for TAM obtaining, each experiment using n = 4 for naïve and n = 4 for post-sepsis. We selected the 4 best within a group of 12 samples, following A260/280 and A260/230 ratios. For bone marrow derived macrophage from naïve and from post-sepsis, and for M1 and M2-polarized macrophage, we conducted two independent experiments using n = 3 per group. The best 4 samples in each group was selected to microarray processing and analysis.

Dataset Information

Gene expression in response to low-intensity pulsed ultrasound treatment of bone marrow cells under osteogenic conditions in vitro

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure