ABSTRACT: Single-cell whole-genome sequencing of primary GBM tumours and matched patient-derived organoids. Obtained using the 10X Genomics single-cell CNV solution. Samples from two spatially distinct regions of five tumours from three patients (three primary, two recurrent).
Project description:Single-cell RNA-seq of primary GBM tumours and matched patient-derived organoids and gliomasphere lines. Obtained using the 10X Genomics single-cell 3' expression solution (v2 chemistry). Primary samples and PDOs from 12 tumours from 10 patients (10 primary, two recurrent), and gliomasphere lines from a subset of five tumours. Samples were obtained from two spatially distinct regions of each tumour.
Project description:Whole-exome sequencing (~250X coverage) of primary GBM tumours and matched patient-derived organoids and normal blood. Samples from two spatially distinct regions of seven tumours from five patients (five primary, two recurrent).
Project description:Glioblastoma (GBM) is a highly heterogeneous malignant brain tumour. We took multi-region spatially separated samples from tumours and isolated invasive GBM cells using FACS based on 5ALA of near normal brain parenchyma. RNAseq was then performed to compare expression profiles for tumour cells from different microenvironment.
Project description:The 16p11.2 is the most common copy number variant (CNV) associated with Autism Spectrum Disorder (ASD). We used patient-derived cerebral organoids to investigate neurodevelopmental pathways dysregulated by dosage changes of 16p11.2 CNV. To investigate molecular dysregulation in DEL and DUP organoids, we carried out RNA sequencing and Tandem Mass Tag mass spectrometry (TMT-MS) on 1-month and 3-month organoids from the same samples. In proteomic analyses, we quantified a total of 6126 proteins in 1-month and 5481 proteins in 3-month organoids, with 13 and 11 proteins from within 16p11.2 CNV, respectively. Transcriptomic and proteomic profiling of organoids identifies the key drivers of functional effect by 16p11.2 CNV during neocortical development.
Project description:Using HiRIEF LC-MS/MS, we analysed 10 GBM tumour tissue samples ran in one TMT10 set. The set consisted of 7 primary tumours and 3 non-matched recurrent tumours. One primary tumour was highly necrotic.
Project description:In study we investigated podocyte maturation, with a particular focus on type IV collagen maturation in the glomerular basement membrane (GBM) of kidney organoids over extended culture periods (comparing Control Organoid d22 R2 with Control Organoid d38). The secondary aim was to compare the gene expression profiles of podocytes in X-linked Alport syndrome (XLAS) organoid models with isogenic controls at an early culture time point (day 22). Two distinct batches of sample collection were conducted to capture early and later stages of GBM development. In the first batch, three libraries were generated by collecting 16 organoids from one isogenic control, one severe XLAS model, and one moderate XLAS model on day 22 of differentiation. In the second batch, two libraries were created to evaluate the impact of culture duration on GBM maturation by harvesting an additional isogenic control organoid at both day 22 and day 38 of culture. Organoids were dissociated using a two-step enzymatic and mechanical protocol to obtain single-cell suspensions, with cell viability ranging between 70% and 85%. This experimental design enabled a comparative analysis of GBM maturation dynamics between early and late time points and across different severities of XLAS. Findings from this study provided insights into the cellular mechanisms underlying GBM abnormalities in Alport syndrome and supported the potential for GBM maturation in kidney organoids over time.
Project description:n this study we had two primary aims: 1.) spatially define the transcriptional signatures of porcine maternal-fetal interface and 2.) develop and validate an organoid model which better recapitulated the porcine placenta. Using mid-gestation maternal-fetal interfaces of commercial landrace/large white composite gilts we performed spatial transcriptomics (n=4 interfaces) using Visium v1 spatial transcriptomics. We then went on to isolate trophoblast organoids from fresh-term placentas from crossbred sows consisting</p><p>655 of Yorkshire, Large White, and Landrace breeds. We then characterized the transcriptional profile of these organoids using bulk RNA-seq from 3 seperate lines using a standard Illumina library preparation. To characterize these organoids we performed single cell RNA-sequencing on 3 separate lines of swine trophoblast organoids using a standard 10x Genomics Single Cell 3' Gene Expression platform. All reads/samples were mapped to Sus scrofa v11.1.
Project description:In this study we had two primary aims: 1.) spatially define the transcriptional signatures of porcine maternal-fetal interface and 2.) develop and validate an organoid model which better recapitulated the porcine placenta. Using mid-gestation maternal-fetal interfaces of commercial landrace/large white composite gilts we performed spatial transcriptomics (n=4 interfaces) using Visium v1 spatial transcriptomics. We then went on to isolate trophoblast organoids from fresh-term placentas from crossbred sows consisting</p><p>655 of Yorkshire, Large White, and Landrace breeds. We then characterized the transcriptional profile of these organoids using bulk RNA-seq from 3 seperate lines using a standard Illumina library preparation. To characterize these organoids we performed single cell RNA-sequencing on 3 separate lines of swine trophoblast organoids using a standard 10x Genomics Single Cell 3' Gene Expression platform. All reads/samples were mapped to Sus scrofa v11.1.
Project description:We collected five DMG, five GBM (including two secondary GBM), and one peritumor samples from eleven patients requiring surgical resection. To establish an atlas for spatially-resolved gene expression, we performed short-read spatial transcriptomic sequencing on the tissue sections using the 10x Visium platform.
Project description:This study aims to compare in vivo human trophoblast differentiation into EVTs to different in vitro trophoblast organoids using single-cell and single-nuclei RNA sequencing. The study includes two type of systems: human primary trophoblast organoids (PTO) and trophoblast stem cells (TSCs). Trophoblast stem cell (TSC) lines BTS5 and BTS11 derived by Okae and colleagues were grown as described previously (Okae et al. 2018) and together with EVT media. Primary trophoblast organoids (PTO) were grown and differentiated into EVT as previously described by Turco & Sheridan (Turco et al 2018; Sheridan et al 2020). This study shows that the main regulatory programs mediating EVT invasion in vivo are preserved in in vitro models of EVT differentiation from primary trophoblast organoids and trophoblast stem cells.
