Tissue Sampling and Biorepository to improve Cancer Cell Therapy
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PROVIDER: PRJNA909908 | ENA |
REPOSITORIES: ENA
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Project description:Tissue Sampling and Biorepository to improve Cancer Cell Therapy
| PRJNA909907 | ENA
Project description:It was recently shown that ultrashort pulse infrared (IR) lasers, operating at the wavelength of the OH vibration stretching band of water, are highly efficient at softly sampling and homogenizing biological tissue. We utilized a nanosecond infrared laser (NIRL) for tissue sampling and homogenization with subsequent LC-MS/MS analysis for mass spectrometric proteomics. Sampling was performed with murine spleen and colon tissue with an ablation volume of 1.1 x 1.1 x0.4 mm³ (approx. 0.5 µl), determined with optical coherence tomography (OCT). The identified proteins of both tissues contained tissue type specific proteins correlating with the corresponding lists of the Human Protein Atlas. The results demonstrate that tissue sampling and homogenization of small tissue volumes less than 1 µL for subsequent mass spectrometric proteomics is feasible with a NIRL and therefore is an alternative towards sampling of tissue sections with laser capture microdissection (LCM).
2022-02-17 | PXD027700 | Pride
Project description:Single-cell transcriptomic sampling of regenerating mouse muscle tissue
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Project description:To achieve a deep quantitative proteomic profiling of whole tissue with the spatial localization preserved, we designed an untargeted spatial proteomics workflow with a sparse sampling strategy. We combined a computational approach and MS-based proteomics analysis to localize high-throughput proteome mapping within a tissue by microdissecting the slices into a series of parallel strips with different angles, that allow subsequent image reconstruction. We successfully reconstructed a whole-tissue mapping in a mouse brain, consisting of 8,645 protein distributions and expressions with a spatial resolution of approx. 300 μm.
2024-12-31 | PXD059321 |
Project description:Ultrasound-guided fine-needle aspiration (US-FNA) biopsy is a widely used minimally invasive sampling procedure for cytological diagnosis. This study investigates the feasibility of using US-FNA samples for both cytological diagnosis and whole transcriptome RNA-sequencing analysis (RNA-Seq), with the ultimate aim of improving canine prostate cancer management. The feasibility of the US-FNA procedure was evaluated intra vitam on 43 dogs. Additionally, aspirates from 31 euthanised dogs were collected for standardising the procedure. Each aspirate was separated into two subsamples: for cytology and RNA extraction. Additional prostate tissue samples served as control for RNA quantity and quality evaluation, and differential expression analysis. The US-FNA sampling procedure was feasible in 95% of dogs. RNA isolation of US-FNA samples was successfully performed using phenol-chloroform extraction. The extracted RNA of 56% of a subset of US-FNA samples met the quality requirements for RNA-seq. Expression analysis revealed that only 153 genes were exclusively differentially expressed between non-malignant US-FNAs and tissues. Moreover, only 36 differentially expressed genes were associated with the US-FNA sampling technique and unrelated to the diagnosis. Furthermore, the gene expression profiles clearly distinguished between non-malignant and malignant samples. This proves US-FNA to be useful for molecular profiling.
2019-10-08 | GSE122916 | GEO
Project description:For investigating the molecular physiology and pathophysiology in organs the most exact data will be obtained, if not organ specific cell lines are analysed or the whole organ is homogenized, followed by the analysis of its biomolecules, but if the morphological organisation of the organ can be addressed and in the best case the composition of molecules in single cells of the target organ can be analysed. Laser capture microdissection (LCM) is a technique, which is enabling the selection of specific cells of a tissue for further analysis of their molecules. However, LCM is a time-consuming 2-dimensional technique and optimal results are only obtained, if the tissue is fixed e.g. by formalin. Especially for proteome analysis formalin fixation is reducing the number of identifiable proteins, which is an additional drawback. Recently, it was demonstrated that sampling of fresh-frozen (non-fixed) tissue with an infrared-laser is giving higher yields with respect to the absolute protein amount and number of identifiable proteins than conventional mechanical homogenization of tissues. In this study the applicability of the infrared laser tissue sampling for proteome analysis of different cell layers of murine intestine was investigated, using LC-MS/MS-based differential quantitative bottom-up proteomics. By laser ablation eight consecutive layers of the colon tissue were obtained and analyzed. Beside a clear distinguishability of protein profiles between ascending, descending and transversal colon, we identified in the different intestinal cell layers proteins, which are cell-specific as confirmed with data from the human protein atlas. Thus, for the first time the sampling directly from intact fresh-frozen tissue with 3-dimensional resolution is giving access to the different proteomes of the different cell layers of colon tissue.
2022-06-22 | PXD033584 | Pride
Project description:We have developed an endovascular catheter-based device for sampling of the endothelium, intended for RNA-seq analysis. With an outer diameter of 0.23 mm it is capable of reaching peripheral vessels for endothelial sampling, and favourably compares to other approaches with stent retrievers or similar tools. Here, we have collected samples from liver and kidney vessels from swine and performed RNA-sequencing to validate the sample quality.
2022-08-21 | GSE197756 | GEO
Project description:Modest target sequencing yield improvements using Nanopore adaptive sampling to reduce human DNA contamination from clinical tissue samples
| PRJEB78709 | ENA