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Expression data from human primary monocyte derived immature dendritic cells (iDC)

ABSTRACT: During HIV-1 infection, iDCs contribute to mounting an immune response and to viral dissemination, however most of the studies addressing iDCs-HIV-1interactions have been performed in standard 2D suspension cultures which do not reflect the 3D architecture of tissues in vivo. To overcome this limitation and to understand the role that the 3D environemt has we studied iDC biology as well as iDC-HIV-1 functional interactions in 3D collagen matrix comparing 3D collagen cultures to standard 2D suspension cultures. We used microarray data to analyze how the 3D environment affects the expression profile of monocyte derived iDCs under basal condition, LPS stimulation and in response to HIV-1 infection

ORGANISM(S): Homo sapiens

PROVIDER: GSE218367 | GEO | 2023/03/28

REPOSITORIES: GEO

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2D and 3D Madin-Darby Canine Kidney Cell Type II cell line response to hepatocyte growth factor

Project description:Analysis of 2D (transwell) and 3D (collagen type I) cultured MDCK cells and HGF (a MAPK activator). Traditional 2D cultures are fast and inexpensive but do no mimic natural niche/cell environment as well as the more laborious and costly 3D-cultures. 3D cultures, arguably, are better models for the study of developmental processes, such as tubulogenesis. Epithelial organs (such as kidney) develop via tubulogenesis, a process, at least in part, regulated by MAPK signaling. Therefore, 2D and 3D cells also treated with HGF plus MAPK inhibitors. Results provide insights into differential response to HGF-induced tubulogenesis depending on cell culture conditions (2D vs. 3D). 29 samples total: 2D and 3D control (untreated) in quadruplicate, respectively; 2D and 3D + HGF in quadruplicate, respectively; 2D + HGF + PD-98059 in quadruplicate; 3D + HGF + PD-98059 in triplicate; 2D + HGF + U0126 in triplicate; and 3D + HGF + U0126 in triplicate.

2014-03-31 | E-GEOD-49518 | biostudies-arrayexpress

2D and 3D Madin-Darby Canine Kidney Cell Type II cell line response to hepatocyte growth factor

2014-03-31 | GSE49518 | GEO

RNA-Seq of ILC and IDC breast cancer cell lines in attached (2D) and suspension (ultra-low attachment) cultures

Project description:RNA-Seq of ILC and IDC breast cancer cell lines in attached (2D) and suspension (ultra-low attachment) cultures

| PRJNA540874 | ENA

RNA-Seq of ILC and IDC breast cancer cell lines in attached (2D) and suspension (ultra-low attachment) cultures

Project description:Invasive lobular carcinoma (ILC) is a histological subtype of breast cancer with distinct molecular and clinical features from the more common subtype invasive ductal carcinoma (IDC). ILC cells exhibit anchorage-independent growth in ultra-low attachment (ULA) suspension cultures, which is largely attributed to the loss of E-cadherin. In addition to anoikis resistance, herein we show that human ILC cell lines exhibit enhanced cell proliferation in ULA cultures as compared to IDC cells. Proteomic comparison of ILC and IDC cell lines identified induction of PI3K/Akt and p90-RSK pathways specifically in ULA culture in ILC cells. Further transcriptional profiling uncovered unique upregulation of the inhibitors of differentiation family transcription factors ID1 and ID3 in ILC ULA culture, the knockdown of which diminished the anchorage-independent growth of ILC cell lines through cell cycle arrest. We find that ID1 and ID3 expression is higher in human ILC tumors as compared to IDC, correlated with worse prognosis uniquely in patients with ILC and associated with upregulation of angiogenesis and matrisome-related genes. Altogether, our comprehensive study of anchorage independence in human ILC cell lines provides mechanistic insights and clinical implications for metastatic dissemination of ILC and implicates ID1 and ID3 as novel drivers and therapeutic targets for lobular breast cancer.

2020-06-23 | GSE130650 | GEO

Effects of culture conditions on epigenomic profiles of brain tumor cells

Project description:We performed epigenomic analysis of brain tumor cells that were collected from micro-engineered three-dimensional tumor models. We used a low-input epigenomic analysis method known as microfluidic-oscillatory-washing-based chromatin immunoprecipitation with sequencing (MOWChIP-seq) to analyze genome-wide histone modification (H3K4me3). We compared H3K4me3 patterns in standard 2D cultures and 3D cultures based on type I collagen hydrogels, under both normoxic and hypoxic conditions. Our work illustrates a direct connection between cell culture or tissue niche condition and genome-wide alterations in histone modification.

2019-02-01 | GSE113824 | GEO

aCGH study of invasive duct carcinoma (IDC) of the breast without axillary lymph node LN and with sentinel LN metastasis

Project description:22 patients with IDC: 8 without LN metastases (IDC) and 14 with sentinel LN metastases (IDCM). Sampling was limited to 29 paraffin blocks which could be used up without interference with diagnostic procedures: 8 IDCs, 11 IDCMs and 10 ipsilateral LN metastases [5 to the sentinel LN (first in lymph drainage chain, MS) and 5 to more distal (MD)]. 7 IDCMs had samples of their LN metastases (IDCM9,13, 14, 15, 17, 18, 19). 3 samples of metastases (MS20, 21, 22) did not have paired primary IDCM samples and 4 IDCMs (IDCM10, 11, 12, 16) did not have samples of their LN metastases. Keywords: Comparative clinical study

2009-02-01 | GSE10600 | GEO

Madin-Darby Canine Kidney (MDCK) cells grown in 2-dimensional and 3-dimensional type I collagen culture.

Project description:In order to gain insight into epithelial morphogenesis and the influence of culture geometry on gene expression patterns, Madin Darby Canine Kidney (MDCK) epithelial cells where grown in 2-dimensional (2D) culture or 3-dimensional (3D) culture . MDCK cells cultured in 2D were plated atop a pre-solidified type I collagen gel. Cells cultured under these conditions grew as flat monolayer sheets. In 3D culture, cells are embedded within type I collagen gel. Cells grown under these conditions form large spherical cysts with hollow central lumens. We anticipate, therefore, that these results provide insight into the mechanisms that regulate epithelial cystogenesis. Cells grown in the 2D or 3D geometries were collected from digested type I collagen gels on day 8. The 2D MDCK cells were treated as the control condition and there gene expression patterns were compared to those of 3D grown cells, which served as the experimental condition.

2013-06-03 | E-GEOD-28381 | biostudies-arrayexpress

Effect of 2D and 3D cell culture system on trophoblast extracellular vesicles physio-chemical characteristics and potency

Project description:In this project, trophoblast cell analogue human chorionic carcinoma cell line was cultivated in both conventional monolayer culture (2D) and as spheroids in suspension cultures (3D) and how the cell growth environment affects the physical and biochemical properties of EVs produced by them was studied. Importantly, proteomic cargo profile of EVs derived from 2D and 3D cultures was compared. There was substantial differences in the proteomic cargo profile and potency of EVs derived from two culture systems. Findings of this study will help in selecting an EV production platform, especially for assessing the functional and therapeutic potential of EVs.

2024-05-08 | PXD048789 | Pride

Gene expression profile of two colorectal cancer HT29 and DLD-1 cell lines treated with single or fractionated ionizing radiation doses under 3D cell culture conditions.

Project description:Tumor cell response to irradiation also depends on their microenvironment. Therefore ongoing investigation of three-dimensional (3D) cell culture models provide researchers with essential data studying and remodeling radiotherapeutic implications in cancer treatment. 3D culture models were shown to mimic in vivo cell microenvironment more accurately than the standard two-dimensional cell monolayer (2D) cultures. Growing evidence suggests that 2D and 3D cultured cell gene expression pattern discrepancies following irradiation is highly dependent on cell-ECM interactions. It has been shown that laminin-rich-extracellular matrix (lr-ECM) used in 3D cultures not only alters cancer cell phenotype and response to external stimuli but also affects their differentiation, migration and survivability. Thus, a change in these fundamental cell properties demands us to reconsider data previously collected using 2D in vitro models. RNA was harvested from two colorectal cancer cell lines cultivated under 3D cell culture conditions, 4h after treatment of single (2 Gy or 10 Gy) or fractionated (5x2 Gy) ionizing radiation dose.

2015-12-12 | E-GEOD-75915 | biostudies-arrayexpress

Gene expression profile of two colorectal cancer HT29 and DLD-1 cell lines treated with single or fractionated ionizing radiation doses under 3D cell culture conditions.

2015-12-12 | GSE75915 | GEO

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