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Temporal transcriptomic analysis of human pancreatic exocrine cells in 3D suspension culture

ABSTRACT: Temporal transcriptomic analysis of human pancreatic exocrine cells in 3D suspension culture

PROVIDER: PRJNA646916 | ENA |

REPOSITORIES: ENA

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Temporal transcriptomic analysis of human pancreatic exocrine cells in 3D suspension culture

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-07-18 | GSE154635 | GEO

Expression data from day of isolation and day 4 suspension cultured human pancreatic exocrine cells

Project description:Donor pancreata were obtained from the Beta Cell Bank of the JDRF Centre for Beta Cell Therapy in Diabetes (Brussels, Belgium), from Pancreatic Islet Processing (ECIT center) of Diabetes Research Institute at the IRCCS San Raffaele Scientific Institute (Milan, Italy) and from the DRWF Human Islet Isolation Facility (Oxford, England). Full written consent for use of donor material for research was obtained according to Belgian, Italian and English laws. This project was approved by the Medical Ethical Committee of all institutions. Cells were cultured in 3D suspension culture for four days in Advanced RPMI supplemented with 5% FBS.

2020-07-18 | GSE154628 | GEO

Expression data from day of isolation and day 4 suspension cultured human pancreatic exocrine cells

Project description:Expression data from day of isolation and day 4 suspension cultured human pancreatic exocrine cells

| PRJNA646903 | ENA

Expression data from of FACS separated acinar and duct cell at day 4 of suspension cultured human pancreatic exocrine cells

2020-07-18 | GSE154629 | GEO

Transcriptomic profiling of DU4475 cells in 3D cell culture matrices and suspension

Project description:Transcriptomic profiling of DU4475 cells in 3D cell culture matrices and suspension

| PRJNA952219 | ENA

Transcriptomic profiling of DU4475 cells in 3D cell culture matrices and suspension

Project description:The extracellular matrix (ECM)-regulated phenotypic plasticity is crucial for metastatic progression of triple negative breast cancer (TNBC). To investigate the effect of matrix cues on phenotypic plasticity, we embedded triple negative DU4475 cells from suspension culture into mechanically tunable fibrin gels or basement membrane extract (Matrigel). Cells in suspension culture and matrix cultures showed divergent gene expression profiles, with specific gene expression signatures depending on the biochemical composition and stiffness of the matrix.

2023-04-05 | GSE228939 | GEO

Soybean Suspension culture analysis

Project description:Proteomic analysis of soybean suspension cell extracellular and intracellular protein

2022-02-22 | PXD001895 | Pride

Exocrine and connective tissue signatures in early pancreatic adenocarcinoma foci and their surrounding tissue

Project description:This project is reporting on microdissection proteomics of human operable, non-neoadjuvant treated pancreatic ductal adenocarcinomas (PDAC) with deep coverage of histologically neoplastic and adjacent healthier exocrine glands as well as stromal regions surrounding both. Through proteomic analysis, the parenchymal sample types differed significantly, with the malignant regions characterized by a broad downregulation of digestive enzymes. Instead, the stromal areas were alike, dominated by extracellular matrix proteins and lower expression of most metabolic pathways compared to the exocrine areas. Cholesterol synthesizing enzymes were more abundant in the tumor than stroma, as confirmed by an independent PDAC dataset and immunohistochemistry of PDAC microarrays. However, this was not accompanied by intratumor lipid deposition. Pathways most prognostic for survival were unexpectedly enriched in the histologically healthier exocrine glands, with a specific prognostic marker. Systematic analysis of pancreatic cancer transcriptomes from The Cancer Genome Atlas revealed that increased transcriptional complexity confers poor prognosis in PDAC.

2022-09-05 | PXD026371 | Pride

Expression data from of FACS separated acinar and duct cell at day 4 of suspension cultured human pancreatic exocrine cells

Project description:Expression data from of FACS separated acinar and duct cell at day 4 of suspension cultured human pancreatic exocrine cells

| PRJNA646904 | ENA

4C-seq: Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

Project description:Hox genes are essential regulators of embryonic development. They are activated in a temporal sequence following their topological order within their genomic clusters. Subsequently, states of activity are fine-tuned and maintained to translate into domains of progressively overlapping gene products. While the mechanisms underlying such temporal and spatial progressions begin to be understood, many of their aspects remain unclear. We have systematically analyzed the 3D chromatin organization of Hox clusters in vivo, during their activation using high-resolution circular chromosome conformation capture (4C-seq). Initially, Hox clusters are organized as single 3D chromatin compartments decorated with bivalent chromatin marks. Their progressive transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch one after the other, from an inactive to an active 3D compartment. These local 3D dynamics occur within a larger constitutive framework of interactions within the surrounding Topological Associated Domains, which confirms previous results that regulation of this process in primarily cluster intrinsic. The local step-wise progression in time can be stopped and memorized at various body levels and hence it may accounts for the various chromatin architectures previously described at different anterior to posterior body levels for the same embryo at a later stage. Circular Chromosome Conformation Capture (4C-seq) samples from mouse ES cells and mouse embryonic samples at different stages of development. Data based on 41 biological samples.

2014-04-28 | E-GEOD-55342 | biostudies-arrayexpress

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