Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Osteosarcoma patient RNA sequencing data matrix

ABSTRACT: This dataset contains processed RNA sequencing expression matrices derived from osteosarcoma patient samples. A total of 40 clinical specimens were analyzed, including 30 primary osteosarcoma tumor tissues and 10 non-sarcoma tissues. Raw sequencing data were preprocessed to generate normalized gene expression matrices suitable for downstream bioinformatic analyses, such as differential expression and pathway enrichment studies.

INSTRUMENT(S): Thermal cycler, Magnetic stand / beads, Pipettes and tips, Microcentrifuge tubes, Plate shaker, Liquid nitrogen, -80°C freezer, Surgical tools (scalpels, forceps), Sample tubes / cryovials, Illumina NovaSeq 6000, Centrifuge, Pipettes and tips, Agilent 2100 Bioanalyzer, NanoDrop spectrophotometer, Vortex mixer, None

ORGANISM(S): Homo sapiens

SUBMITTER: Zehao Guo

PROVIDER: E-MTAB-15886 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The fibroblast-populated 3D collagen matrix has been used to study the effect of mechanical stress on cell fate; this process is relevant to the fields of wound healing and tissue engineering. Gene array data was generated from mechanically stressed vs. stress-released matrices. The parameters of the collagen matrix model were: collagen type = bovine type I; collagen concentration = 1.5 mg/mL; initial matrix volume = 0.2 mL; initial matrix diameter = 11 mm (cultured in 24-well plates); cell type = human foreskin fibroblast, passage <10; initial matrix cell concentration = 1,000,000 cell/mL (200,000 cell/matrix); culture medium = 5% FBS in DMEM with 1 M-BM-5g/mL ascorbate. Matrices (n = 6 per experimental group) were incubated for 24 hr in the attached state; the released groups then underwent matrix detachment from the culture plate (defined as t = 0), while the attached groups were left undisturbed. RNA was isolated from attached and released matrices 6 and 24 hr after t = 0. Gene expression in the attached vs. released condition at 6 or 24 hr then was analyzed by hybridizing the anti-sense RNA derived from attached and released matrices at a given time point onto a single chip. Refer to the attached Figure 1 for the experimental design. The index experiment was defined as the comparison of gene expression in attached vs. released collagen matrices in a single strain of human foreskin fibroblasts at 6 and 24 hr after stress-release (i.e., after t = 0). Each experiment utilized two mechanical conditions (attached and released) at two time points (6 and 24 hr). So with each condition utilizing 6 matrices, each index experiment required a total of 24 matrices. In each index experiment, the chip hybridizations were: (i) 6 hr attached vs. 6 hr released, and (ii) 24 hr attached vs. 24 hr released (i.e., two gene chips per index experiment). Each hybridization was done using a 10K spotted gene chip manufactured in the UNMC Microarray Core Facility. The index experiment was performed on three fibroblast strains, meaning that expressional data was derived from three foreskin donors (nonpooled samples). Dye-swap was not performed; dye assigned to attached vs. released remained constant among all chips. Since the index experiment was performed three times, the total number of gene chips used for this entire dataset was six.

Dataset Information

Osteosarcoma patient RNA sequencing data matrix

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