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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide analysis of gene expression changes in human alveolar epithelial cells grown on collagen- or matrigel-coated dishes

ABSTRACT: Analysis of human alveolar epithelial cell signatures at gene expression level. The aim of the study was to identify candidate genes that are induced in human alveolar epithelial type II cells on collagen-coated dishes. Results provide important information about changes hAT2 cells undergo in the transformation to AT1-like cells. Total RNA obtained from human alveolar epithelial cells grown on collagen- or matrigel-coated dishes for 12, 24, 48 and 72 hr.

ORGANISM(S): Homo sapiens

SUBMITTER: Helena Morales Johansson

PROVIDER: E-GEOD-40516 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis of gene expression changes in human alveolar epithelial cells grown on collagen- or matrigel-coated dishes

Project description:Analysis of human alveolar epithelial cell signatures at gene expression level. The aim of the study was to identify candidate genes that are induced in human alveolar epithelial type II cells on collagen-coated dishes. Results provide important information about changes hAT2 cells undergo in the transformation to AT1-like cells.

2014-02-01 | GSE40516 | GEO

Genome-wide analysis of gene expression changes in human alveolar epithelial cells grown on collagen- or matrigel-coated dishes

2014-02-01 | GSE40516 | GEO

Gene expression of rat PSCs cultured on plastic, matrigel and collagen

Project description:Activated pancreatic stellate cells produce the fibrotic matrix in chronic pancreatitis and pancreatic cancer. In vitro protocols examining PSC biology have usually involved PSCs cultured on plastic, a non-physiological surface. However, PSCs cultured on physiological matrices e.g. MatrigelTM (normal basement membrane) and collagen (fibrotic pancreas), may have distinctly different behaviours compared to cells cultured on plastic. Therefore, we aimed to compare PSC gene expression after culture on plastic, MatrigelTM and collagen I. Total RNA from stellate cells in 10 cm Petri dishes was isolated by Qiagen RNeasy Mini Plus kit as per manufacturer’s instructions. The Agilent 2100 Bioanalyzer (Agilent Technologies Inc. Santa Clara, CA) was used for quality control of the isolated total RNA. Gene expression profiles of rat PSCs cultured on MatrigelTM, collagen I and plastic were analysed by whole rat genome microarray purchased from Affymetrix (Rat Gene 1.0 ST Array). This array was able to detect 27,342 rat genes, with approximately 26 probes on average per gene (referred to as a probe set).

2013-01-17 | E-GEOD-43496 | biostudies-arrayexpress

RNA-seq of wildtype mouse small intestinal organoids grown in Matrigel or in/on collagen.

Project description:We aimed to analyse the effect of different extra-cellular matrices on the growth of small intestinal organoids. Small intestinal crypts of wildtype mice were harvested and grown under standard Matrigel organoid conditions. After establishment of organoids (passaged 1-2), organoids were grown in Matrigel, on collagen or in a drop of collagen. Growth in a droplet of collagen requires addition of Wnt3a, therefore all samples are either provided with standard culture conditions (ENR) or with ENR+50%Wnt3a-CM (WENR). Samples were grown in specified matrix for at least 1-2 passages before RNA was purified.

2021-04-01 | E-MTAB-10082 | biostudies-arrayexpress

Murine host body reactions to implanted scaffolds: non-coat polystyrene scaffold vs. collagen- or PMB-coated scaffold

Project description:This study investigated early host reactions to implanted materials to predict successful tissue regeneration with implant. Three kinds of scaffold, i.e., non-coat, collagen-coated, and PMB-coated porous polystylene scaffolds were implanted subcutaneously in mice dorsal area. Those scaffolds were used as bio-incomopatible materials, appropriate materials for tissue regeneration (bio active), and inappropriate to regenration (bio-inert) scaffolds. Seven days after implantation, scaffolds were explanted and total RNA was isolated from infiltrated host cells into scaffold by laser microdissection. Gene expressions of cells in collagen- and PMB-coated scaffold were normalized using results of non coat scaffold. Genes with more than 2-fold difference between collagen and PMB were picked up and narrowed to related keywords; inflammation, angiogenesis, wound healing, and mcrophage polarization. Among those genes, interluekin (IL)-1beta which promote both inflammation and wound healing was up-regulated in collagen-coated scaffold. On the other hand, IL-10 which suppress both inflammation and wound healing was up-regulated in PMB-coated scaffold. Angiogenesis-promoting genes were up-regulated and angiogenesis suppressve genes were suppressed in collagen. Up-regulation of IL-1b and the angiogenesis-relating genes inside the porous scaffolds are the possibly important factors for controlling tissue regeneration. Three-condition experiment, host cells infiltrated in non coat (reference), collagen-coated, and PMB-coated scaffolds. Two-microarray condition experiments, collagen vs. non coat and PMB coat vs. non coat. Hybridization: 2 replicates. Scanning: 3 replicates. Biological experiments: once.

2014-01-23 | E-GEOD-52053 | biostudies-arrayexpress

Homo sapiens

Project description:Genome-wide analysis of gene expression changes in human alveolar epithelial cells grown on collagen- or matrigel-coated dishes

| PRJNA174206 | ENA

Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation (Rat)

Project description:Analysis of gene expression during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells. Timepoints taken at Day 0 (AT2 cell), Days 2, 4, and 6 in culture (differentiating) and Day 8 in culture (AT1-like cells). 1ug of RNA was subjected to cRNA conversion using Illumina TotalPrep RNA kit and hybridized to the HT12v4 array Analysis of gene expression during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells

2013-04-15 | E-GEOD-38570 | biostudies-arrayexpress

Murine host body reactions to implanted scaffolds: non-coat polystyrene scaffold vs. collagen- or PMB-coated scaffold

2014-01-23 | GSE52053 | GEO

RNA-seq analysis of mESCs cultured on either Laminin-511 or gelatin coated dishes in either Std or 2i medium

Project description:Some mouse embryonic stem cell (mESC) lines need to be maintained on feeder cells in gelatin/Std condition. To eliminate the need for feeder cells, we decided to maintain the C57BL6/J mESCs on dishes coated with Laminin-511 (LN511) enabling maintenance of mESCs without feeder cells in Std condition (Domogatskaya et al., 2008). To compare the transcriptomes of mESCs cultured on gelatin-coated dish and those cultured on Laminin-511 coated dish, we performed RNA-Seq analysis. We found that the transcriptomes of mESCs cultured on gelatin-coated dish and those cultured on LN511 coated dish showed no considerable difference in expression patterns.

2020-06-04 | GSE132591 | GEO

Gene expression profile of human embryonic stem cell-derived hepatocyte-like cells in matrigel and recombinant laminins

Project description:Stem cell derived somatic cells represent an unlimited resource for basic and translational science. While promising, there are significant hurdles that must be overcome. Our focus is on the generation of the major cell type of the human liver, the hepatocyte. Current protocols produce variable populations of hepatocytes, which is the product of using undefined components in the differentiation process. To tackle this issue, we have designed a defined differentiation process using recombinant laminin substrates as extracellular matrix support, and compared the hepatic differentiation potential obtained with this matrix to that of matrigel. Human embryonic stem cells H9 were replated onto matrigel, pure laminin 521 and the laminin 521:111 mix (1:3 ratio, referred to as laminin 111 mix) coated wells.

2016-01-18 | E-MTAB-3994 | biostudies-arrayexpress

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