Project description:Naive B cells cultured in the presence of IL-2 and IFN-g (Be-g2) leads to a distinct programming outcome. To determine the epigenetic programming changes during Be-g2 differentiation ATAC-seq was performed on Be-0, Be-IL2, Be-IFNg, and Be-g2 cells. These data define the chromatin accessibility landscape of Be-g2 cells and the changes that occur during thier differentiation.
Project description:Prospective, open labelled, multicenter trial to evaluate the feasibility of ex vivo culture 3D (chemogram obtaining) on biopsies in order to estimate the predictive value of this technique for treatment response in patients treated by two different chemotherapies (FOLFOX or FOLFIRI) for colorectal cancer.
Project description:Triplicate samples of donor matched ex vivo generated macrophage subtypes M1, M2a, M2c compared against the M0 control analysed using TMT-based 11plex quantitative proteomics.
Project description:Triplicate samples of donor matched ex vivo generated macrophage subtypes M1, M2a, M2c compared against the M0 control analysed using TMT-based 11plex quantitative proteomics.
Project description:The aim of this study is to compare the transcriptomic profiles of various ex vivo models of pancreatic cancer. First, primary tumours and their corresponding xenografts in nude mice were analysed by RNA-seq. Monocultures of pancreatic cancer cells derived from the xenografts were then prepared as 2D monolayers, Matrigel-embedded organoids, spheres in suspension and 3D cultures in self-assembling peptide amphiphile (PA) hydrogels. Seven-day cultures were then analysed by RNA-seq. The results suggest that all ex vivo monocultures retain patient-specific transcriptional profiles, especially cancer stem cell signatures, while being deficient in the expression of stromal components such as the core matrisome. Correlations with the primary tumours were generally higher in PA hydrogels than organoids. Biased gene expression signatures were identified in certain models. This is the first study to explore the transcriptomic signatures of four different ex vivo models matched to their primary tumours of origin.
Project description:Human in vivo skin wound: Non-wounded skin was obtained by taking punch biopsies from three healthy donors (donor 1,2 and 3). The samples were termed 'skin day 0 in vivo wound'. Skin wound samples were retrieved by making new punch biopsies from the edge of the original biopsies after four days. These samples were termed 'skin day 4 in vivo wound'. As much dermal tissue as possible was removed by dissection to make sure mainly epidermis was present in the samples. The samples were washed in NaCl to possible remove infiltrating inflammatory cells before RNA isolation. Ex vivo skin wounds: Skin was obtained from three healthy donors following reduction surgery (donor 1, 2, and 3). As much dermal tissue as possible was removed dissection. These samples were termed 'skin day 0 ex vivo wound'. Skin was sliced into 1x10 mm slices and incubated in keratinocyte medium for four days with either 1:1000 fold dilution of DMSO or 10 micromolar AG-1478 (dissolved in DMSO). Again as much dermal tissue was removed by dissection as possible before RNA was isolated. These samples were termed 'skin day 4 ex vivo wound' and 'skin day 4 AG-1478 ex vivo wound'. By comparing the gene expression day 4 in ex vivo wound with in vivo wounds it was possible to see which part of the gene expression in wounded skin that was due to the epidermal reaction to injury and how much was due to stimuli from infiltrating inflammatory cells absent in the ex vivo skin wounds. By comparing the data from ex vivo skin wounds day 4 with and without the EGFR-inhibitor AG-1478, it was possible to look at the importance of the EGF-receptor of EGFR for the gene expression in ex vivo wounded skin.
Project description:Triplicate samples of donor matched ex vivo generated macrophage subtype M1 cells treated with and without dexamethasone compared against the M0 control analysed using TMT-based 11plex quantitative proteomics.
Project description:Triplicate samples of donor matched ex vivo generated macrophage subtype M1 cells treated with and without dexamethasone compared against the M0 control analysed using TMT-based 11plex quantitative proteomics.