Study of the consistency, comparability and identity of different Dendritic cells productions for clinical use
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE31195 | GEO | 2012/11/16
SECONDARY ACCESSION(S): PRJNA144757
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression profiling of monocyte-derived Dendritic cells manufactured several times from one healthy donor and one single time from 8 different healthy donors to test the sources of variability Sources tested: Assay-related variability (8 samples), Manufacture-related variability (5 samples), Intra-donor-related variability (5 samples), inter-donor-related variability (9 samples) 4 different levels of variability were accounted: Assay, manufacture, intradonor, and interdonor
2012-11-16 | E-GEOD-31195 | biostudies-arrayexpress
Project description:To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms and methods to accommodate this variability. RNA expression data were generated in seven laboratories, comparing two standard RNA samples using twelve microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor. Reproducibility between laboratories dramatically increased when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization. Nonetheless, concordance could be found across different laboratories and platforms when data were analyzed in terms of enriched Gene Ontology categories. These findings indicate that microarray results generated by multiple sites and platforms can be comparable, and that multi-investigator teams will maximize data comparability by adopting a common platform and a common set of procedures to generate compatible data. Keywords: other
2005-04-21 | GSE2458 | GEO
Project description:Background: Pooled AB serum is often used as a media supplement for cell culture but it has the potential to transmit infectious diseases. To avoid this risk, we used autologous plasma as a media supplement for manufacturing dendritic cells (DCs) for cancer immunotherapy. We noticed inconsistences in the DCs and investigated its nature and cause. Methods: adHER2/neu DCs for 21 patients were manufactured from autologous peripheral blood monocytes which were treated with G-CSF and IL-4 for 3 days, transduced with Ad5f35HER2ECTM and then treated with lipopolysaccharide and IFN- for one day. The cells were cultured in RPMI-1640 supplemented with either 10% heat inactivated autologous or AB plasma. Results: Twenty-eight adHER2/neu DCs were manufactured for 21 patients using autologous plasma and 68 were manufactured for 20 of those patients using AB plasma. The expression of HER2/neu was less for DCs manufactured with autologous plasma (70.3±33.3% vs 86.1±22.8%, p<0.01). Manufacturing adHER2/neu DCs using monocytes from 3 healthy subjects and plasma from one patient with low HER2/neu expression (18%) resulted in low HER2/neu expression by all three DCs (13%, 16% and 23%). Analysis of the levels of 1322 proteins in 8 plasma samples associated with low HER2/neu expression and in 12 associated with high HER2/neu expression revealed that the levels of 14 predicted HER2/neu transduction efficiency. Conclusion: The manufacture of adHER2/neu DC using autologous plasma as a media supplement resulted in inconsistent HER2/neu expression. It is likely that variability in the levels of multiple proteins in autologous plasma contributed to low HER2/neu expression.
2018-12-17 | GSE108225 | GEO
Project description:To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms and methods to accommodate this variability. RNA expression data were generated in seven laboratories, comparing two standard RNA samples using twelve microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor. Reproducibility between laboratories dramatically increased when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization. Nonetheless, concordance could be found across different laboratories and platforms when data were analyzed in terms of enriched Gene Ontology categories. These findings indicate that microarray results generated by multiple sites and platforms can be comparable, and that multi-investigator teams will maximize data comparability by adopting a common platform and a common set of procedures to generate compatible data. Keywords: other
2010-06-10 | E-GEOD-2458 | biostudies-arrayexpress
Project description:Traditional sources of NK cells, such as peripheral blood, are limited by availability and donor variability. Additionally, in vitro expansion can lead to functional exhaustion and gene editing challenges. This study aims to harness iPSC technology to provide a consistent and scalable source of NK cells, overcoming the limitations of traditional sources and enhancing the potential for cancer immunotherapy applications.
2024-09-13 | GSE271952 | GEO
Project description:Human donor derived retinal pigment epithelial cells from healthy, diseased, and disease-modeled sources underwent RNA-sequencing to identify unique, gene signatures.
2019-02-16 | GSE126633 | GEO
Project description:The corneal endothelium plays a primary role in maintaining corneal homeostasis and clarity, and must be surgically replaced with allogenic donor corneal endothelium in the event of visually significant dysfunction. However, a worldwide shortage of donor corneal tissue has led to a search for alternative sources of transplantable tissue. Cultured human corneal endothelial cells (HCEnC) have been shown to restore corneal clarity in experimental models of corneal endothelial dysfunction in animal models, but characterization of cultured HCEnC remains incomplete. To this end, we utilized next-generation RNA sequencing technology to compare the transcriptomic profile of ex vivo human corneal endothelium (evHCEnC) with that of primary HCEnC and HCEnC lines, and to determine the utility of cultured and immortalized corneal endothelial cells as models of in vivo corneal endothelium. Multidimensional analyses of the transcriptome datasets demonstrated that primary HCEnC have a closer relationship to evHCEnC than do immortalized HCEnC. Subsequent analyses showed that the majority of the genes specifically expressed in HCEnC (not expressed in ex vivo corneal epithelium or fibroblasts) demonstrated a marked variability of expression in cultured cells compared with evHCEnC. In addition, genes associated with either corneal endothelial cell function or corneal endothelial dystrophies were investigated. Significant differences in gene expression and protein levels were observed in the cultured cells compared with evHCEnC for each of the genes tested except for AGBL1 and LOXHD1, which were not detected by RNA-seq or qPCR. Our transcriptomic analysis suggests that at a molecular level primary HCEnC most closely resemble evHCEC and thus represent a viable therapeutic option for managing corneal endothelial dysfunction. Our findings also suggest that investigators should perform an assessment of the entire transcriptome of cultured HCEnC prior to determination of the potential clinical utility of the cultured HCEnC for the management of corneal endothelial cell failure. Transcriptomes from ex vivo corneal endothelium, primary cultures and three cell lines were compared. Three samples of each endothelial cell group were submitted for RNA sequencing for a total of 15 samples. The transcriptome for the ex vivo corneal endothelium was used as the reference (i.e., proxy for in vivo corneal endothelium). Transcript abundances for a subset of genes associated with corneal endothelial cell function or disease were validated with qPCR and western blot. Samples of ex vivo endothelium used for validation were independent replicates not used for RNA-sequencing.
2015-09-04 | E-GEOD-65991 | biostudies-arrayexpress
Project description:The experiment consists of 31 Systemic Lupus Erythematosus patient blood samples and 29 healthy donor blood samples.
2018-03-21 | GSE112087 | GEO
Project description:we propose a two-stage procedure for pre-expanding hematopoietic progenitor cells and subsequent ex vivo differentiation for potential granulocyte transfusion. We compared three distinct donor sources, UCB, BM live donor, and BM deceased donor, and tested two expansion different expansion protocols. Donor sources were evaluated based on proliferation during expansion and differentiation phases, neutrophil cell yield, and function. We show that cell for cell, UCB is the most proliferative and give the greatest neutrophil yield. Further, our ex vivo-generated neutrophils of all three donor sources have an enhanced propensity for opsonin-recognizing functions relative to primary neutrophils, which may influence future treatment.
2024-11-13 | GSE273791 | GEO
Project description:The UCSF Treg cell therapy program manufactured over 60 human regulatory T cell (Treg) products under the GMP condition in support of 9 clinical trials between 2011 and 2021. These products were manufactured using two alternative protocols of either two rounds of polyclonal stimulations (PolyTregs) or first allogeneic B cell stimulation followed by polyclonal stimulation (arTregs). A high degree of individual variability in Treg expansion with both protocols was observed. RNA-seq analysis was performed on freshly isolated peripheral blood Tregs to identify transcriptome profile associated with Treg expansions.
2024-04-17 | GSE208111 | GEO