Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA170970 | ENA |
REPOSITORIES: ENA
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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.
2012-07-19 | E-GEOD-39475 | biostudies-arrayexpress
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 µg/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.
2012-07-20 | GSE39475 | GEO
Project description:Human Foreskin Fibroblasts-Trypanosoma cruzi infectome
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Project description:Grobal gene expression of fibroblast populated collagen gel models
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Project description:We report RNA sequencing data from 2 cancer cell line (fibrosarcoma, HT1080 and Breast cancer, MDA-MB-231) and one non-canceours cell line (human foreskin fibroblast HFF) embbeded in two different 3D collagen matrix environements. The topographical organization of collagen within the tumor ECM has been implicated in guiding cancer cell migration and independently predicts progression to metastasis. Here, we show that collagen matrices with small pores and short fibers, but not Matrigel, trigger a conserved transcriptional response and subsequent motility switch in cancer cells that results in formation of multicellular network structures. The response is not mediated by hypoxia, matrix stiffness, or bulk matrix density, but by matrix architecture and beta1 integrin upregulation. The transcriptional module associated with network formation is enriched for migration and vasculogenesis-associated genes that predicted survival in patient data across nine distinct tumor types. Evidence at the protein level of this gene module is found in patient tumors displaying a vasculogenic mimicry (VM) phenotype. Our findings link a collagen matrix-induced migration program to VM, and suggest that this process may be broadly relevant to metastatic progression in solid human cancers.
2017-11-26 | GSE101209 | GEO
Project description:Gene expression profile of collagen VI deficient human fibroblasts
| PRJNA244398 | ENA
Project description:Spheroid Formation and Recovery of Human Foreskin Fibroblasts at Ambient Temperature
| PRJNA104599 | ENA
Project description:Expression data from Human foreskin fibroblasts (HFFs) infected with Toxoplasma gondii.
| PRJNA142585 | ENA
Project description:Expression profiling of human foreskin fibroblasts cultured in media supplemented with human sera
| PRJNA178207 | ENA