Mapping of matrsisome production by alveolar epithelial cells cultured in decellularized human lung scaffolds
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA790837 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17279100_1.fastq.gz | Fastqsanger.gz | |||
| SRR17279100_2.fastq.gz | Fastqsanger.gz | |||
| SRR17279101_1.fastq.gz | Fastqsanger.gz | |||
| SRR17279101_2.fastq.gz | Fastqsanger.gz | |||
| SRR17279102_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 142 |
Similar Datasets
Project description:The alveolar epithelial cells are known producers of basement membrane components of the ECM, we hypothesize that they may also contribute substantially to remodeling of interstitial ECM in the alveolar compartment in chronic lung diseases such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Primary human alveolar type II epithelial cells (AECII) were isolated from human lungs without lung disease or with end stage COPD, using the surface marker HT2-280. Isolated cells were cryopreserved without prior expansion and then directly seeded into decellularized distal lung parenchyma from healthy human lungs. Cells were cultured for 13 days with addition of a profibrotic stimuli in the form of 2 ng/ml of TGF-ß1 at day 7, to a subgroup samples with cells derived from healthy lungs. AECII cells comes from 5 healthy cell donors and 3 with COPD, decellularized scaffolds were prepared from 5 different healthy lungs. The data set contains a total of 71 samples each representing a unique cell/scaffold/treatment combination at either day7 or day 13 of culture. For each sample there exists a matched proteomics sample from mass spectrometry analysis deposited to the ProteomeXchange Consortium via the PRIDE partner repository. The data indicate a substantial potential of alveolar epithelial cells to directly contribute to matrisome turnover and ECM remodeling in the lung.
2022-10-31 | GSE191279 | GEO
Project description:In this study we developed highly proliferative and lineage restricted lung endothelial derived progenitor-like cells using the transient expression of Yamanaka factors via doxycycline inducible system combined with LIF-supplemented media. We investigate the potential of these induced progenitor-like cells for the vascular engineering of the lungs. Our results show that these cells recapitulate the segment specific heterogeneity in the decellularized lung scaffolds and show immediate recovery of endothelial genes after recellularization.
2020-06-23 | E-MTAB-8394 | biostudies-arrayexpress
Project description:Microarray analysis was used to evaluate expression differences from a single donor human bone marrow stromal cells (hBMSCs) as a function of varied polymer-based tissue engineering scaffolds. These scaffolds include polycaprolactone (PCL) nanofibers (PCL_NF), films (PCL_SC), poly D,L-lactic acid (PDLLA) nanofibers (PDLLA_NF), films (PDLLA_SC), tissue culture polystyrene (TCPS) and TCPS with osteogenic supplements (TCPS_OS). The results revealed that scaffold structure was able to significantly affect gene expression, with nanofiber scaffolds inducing similar gene expression patterns to hBMCSs cultured with osteogenic media. A library of scaffolds prepared from polycaprolactone or poly D,L-lactic acid was sythesized and cultured with hBMSCs for 14 days with RNA extracted from cells on Day 1 and Day 14. Gene expression analysis was performed using BRB ArrayTools. SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements. This data forms is part of a pending publication: Baker et al. Ontology Analysis of Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films and is a subset of the 72 array data referenced in ( Kumar et al. The determination of stem cell fate by 3D scaffold structures through the control of cell shape, Biomaterials (2011) 32, 9188-9196.) The 72 array data set is submitted separately to GEO as GSE50743.
2013-11-01 | E-GEOD-50744 | biostudies-arrayexpress
Project description:Microarray analysis was used to evaluate expression differences from a single donor human bone marrow stromal cells (hBMSCs) as a function of varied polymer-based tissue engineering scaffolds. These scaffolds include polycaprolactone (PCL) nanofibers (PCL_NF), films (PCL_SC), poly D,L-lactic acid (PDLLA) nanofibers (PDLLA_NF), films (PDLLA_SC), tissue culture polystyrene (TCPS) and TCPS with osteogenic supplements (TCPS_OS). The results revealed that scaffold structure was able to significantly affect gene expression, with nanofiber scaffolds inducing similar gene expression patterns to hBMCSs cultured with osteogenic media.
2013-11-01 | GSE50744 | GEO
Project description:The liver is the most common site for colorectal cancer (CRC) metastasis and new tissue culture models are needed to study hepatic metastasis from CRC as none of the current models mimic the biological, biochemical and structural characteristics of the metastatic microenvironment. Decellularization provides a novel approach for the study of cancer extracellular matrix (ECM) as decellularized scaffolds retained their tissue-specific features and biological properties. In the present study we created a 3D model of CRC and matched CRC liver metastasis (CRLM) using patient-derived decellularized ECM scaffolds seeded with HT-29 CRC cell line. Here we show increased HT-29 cell proliferation and migration capability when cultured in cancer-derived scaffolds compared to same-patient healthy colon and liver tissues. CRLM scaffolds also induced activation of epithelial-mesenchymal transition (EMT) with cancer cells showing loss of E-cadherin expression and increased Vimentin expression. EMT was confirmed by gene expression profiling, with the most represented biological processes in CRLM-seeded scaffolds involving demethylation, deacethylation, cellular response to stress metabolic processes, response to oxygen level and to starvation. The complex 3D culture environment reduced the HT-29 cell response to anti-CRC drug 5-FU when used at standard IC50 determined in 2D cultures. In conclusion, our 3D culture system with patient-derived tissue-specific decellularized ECM better recapitulates the metastatic microenvironment compared to conventional 2D culture conditions and represents a relevant approach for the study of liver CRC metastasis formation and progression. Transcriptomic analysis was performed comparing the global gene expression profiles of HT29 cells grown on CRLM and HL scaffolds. The transcriptomic profile of each 3D subtype was compared with HT29 cells grown in plastic. Hierarchical clustering analysis revealed that the gene expression signature of recellularized CRLM scaffolds was more comparable to recellularized HL scaffolds, than to HT29 cells grown in 2D. Gene set enrichment analysis (GSEA) of the differently expressed genes (DEG) up-regulated in recellularized CRLM scaffolds compared to HT29 grown in 2D revealed that genes involved in demethylation, deacethylation and metabolic process belong to the most enriched biological pathways in repopulated-CRLM scaffolds. Comparing the DEG between recellularized CRLM scaffolds vs HT29 grown in 2D with a series of a-priori defined gene-set, called Hallmark, we obtained concordant results with the “HYPOXIA” and “EPITHELIAL_MESENCHYMAL_TRANSITION” pathway, enriched in recellularized CRLM, supporting the idea that 3D culture models are the ability to re-create a complex environment in terms of oxygen tension, nutrients, and metabolic gradient, similarly to the in vivo environment.
2019-11-30 | GSE125404 | GEO
Project description:A genomic expression comparison was done among neural progenitor cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and as 3D neural spheres (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level Neural progenitor cells were cultured on 2D surfaces, in 3D scaffolds and as 3D neural spheres. Chemical cues are controlled by coating. Only spacial properties of the culture systems were compared.
2009-12-22 | E-GEOD-13715 | biostudies-arrayexpress
Project description:In this study we have focused on the biomechanical properties of scaffolds (decellularized lung tissue) derived from healthy individuals and IPF patients. The longitudinal cellular response of scaffold repopulation with healthy fibroblasts has been quantified using SILAC-MS. Increased scaffold density and stiffness along with differential expressions of proteins clearly separated and defined ECM proteins descriptive for IPF respective healthy scaffolds. Our study aim to understand the role of the ECM in the development of IPF. We have used proteomics to define intrinsic scaffold ECM proteins descriptive for healthy respective IPF scaffolds. To evaluate whether these mediators directs or rejects profibrotic responses fibroblasts repopulated on healthy and IPF derived scaffolds were cultured in heavy labeled medie (SILAC) to differentiate between preexisting scaffold proteins and newly synthesized proteins. The spatial distribution of unique ECM proteins characteristic for healthy fibroblasts on IPF scaffolds were verified with histological staining.
2019-08-27 | PXD012322 | Pride
Project description:Microarray analysis was used to evaluate expression differences from a single donor human bone marrow stromal cells (hBMSCs) as a function of varied polymer-based tissue engineering scaffolds. The results revealed that gene expression patterns of hBMSCs grouped according to scaffold. A library of scaffolds prepared from polycaprolactone (PCL) or poly D,L-lactic acid (PDLLA) was sythesized and cultured with hBMSCs for 14 days with RNA extracted from cells on Day 1 and Day 14. Gene expression analysis was performed using BRB ArrayTools. GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements. The 72 arrays data was used previously in the publication: Kumar et al. The determination of stem cell fate by 3D scaffold structures through the control of cell shape, Biomaterials (2011) 32, 9188-9196. A companion data set of 24 arrays was submitted separately to GEO as GSE50744 and will be referenced to Baker et al. Ontology Analysis of Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films
2013-11-01 | E-GEOD-50743 | biostudies-arrayexpress
Project description:A genomic expression comparison was done among neural progenitor cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and as 3D neural spheres (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level
2009-12-23 | GSE13715 | GEO
Project description:We investigated whether in vitro expansion of human alveolar epithelial type II cells is possible. We found that human endogenous human alveolar epithelial type II cells can be cultured and passaged. The culture system enabled retroviral gene transduction into human alveolar epithelial type II cells. We performed RNA sequencing of human alveolar epithelial type II cells transduced with mutant surfactant protein C or control vector.
2019-06-27 | GSE128291 | GEO