Project description:RNA-seq of differentiated organoids (day 7) from a patient with an AGR2 mutation, patients with ulcerative colitis, or non-IBD controls. After 6 days differentiation, organoids were treated for 24 hours with Tunicamycin (T7765, Sigma Aldrich,1 µg/ml) or vehicle control (0.1 % DMSO).
Project description:Seeds of Pisum sativum L. cv Alaska Early (purchased from the ‘Abundant Life Seed Foundation’, Port Townsend, USA) were equilibrated for approximately 5 weeks in tightly sealed boxes over 300 g-1 non-saturated LiCl (Hay et al. 2008), producing 60% relative humidity, in a temperature-controlled room (20 ± 1 ºC) until their water potential was stable at 12 % MC. Relative humidity was recorded with a Rotronic AWVC-D10 Hygropalm. These equilibrated seeds are referred to as 0 day ‘non-aged controls’. Following equilibration, accelerated ageing was carried out by placing seeds in sealed bottles at 50 °C until viability loss, thereafter referred to as ‘ageing’. Samples were taken at intervals after 8, 12, and 15 days of ageing. At each interval, germination tests were performed on 1 % water agar at 25 °C under warm white fluorescent light (15 micromol m-2 s-1) at a day / night cycle (8/16h). Germination was defined as radical emergence by at least 2 mm. To summarize, we have performed a transcriptional profiling of Pisum sativum seeds comparing 0 day ‘non-aged controls’ with 8, 12 and 15 days of artificially aged seeds.
Project description:To investigate whether conditioned medium (CM) from cancer cell culture impacts dynamic changes of the transcriptome in myotubes differentiated from hMuSC, we ran RNA sequencing from differentiated hMuSC that were treated by multiple breast cancer cell lines-conditioned medium. Among 14208 readable mRNAs, MCF-7 CM treatment induced significant changes in 2680 genes, MB-468 CM caused significant changes in 2674 genes, and SKBR-3 CM resulted in significant changes in 1823 genes in myotubes from differentiated hMuSC, compared to control group, respectively. Among them, 961 genes had significant upregulation or downregulation presented in differentiated myotubes over all 3 breast cancer cell lines CMs
Project description:Progenitors in human vasculature expanded in-vitro were differentiated with adipogenic cocktail for 12 days, following which they were stimulated with forskolin for 7 days Microarrays were used to detail the program of differentiation of thermogenic human adipose cells
Project description:Progenitors in human vasculature expanded in-vitro were differentiated with adipogenic cocktail for 12 days, following which they were stimulated with forskolin for 7 days Microarrays were used to detail the program of differentiation of thermogenic human adipose cells
Project description:Inorganic arsenic, a ubiquitous environmental contaminant of food and drinking water, is a human carcinogen associated with lung, liver, prostate, renal, and bladder cancers. It has been postulated that inorganic arsenic targets stem cells or partially differentiated progenitor cells, causing their oncogenic transformation. This is proposed to be one of the key mechanisms in arsenic-associated carcinogenesis; however, the underlying mechanisms for this process remain largely unknown. To address this question, human liver HepaRG cells, at progenitor and differentiated states, were continuously treated with a non-cytotoxic concentration of 1 μM sodium arsenite (NaAsO2). Briefly, in Experiment 1, three days after the initial seeding, 1 μM NaAsO2 was added to the media and the cells were maintained in the NaAsO2-containing media for an additional 25 days. In Experiment 2, fourteen days after the initial seeding, 1 μM NaAsO2 was added to the media and the cells were maintained in the NaAsO2-containing media for an additional 14 days. In Experiment 1 and Experiment 2, control and NaAsO2-treated cells were harvested on the 28th day after the initial seeding. In Experiment 3, twenty-eight days after the initial seeding, the terminally-differentiated cells were treated continuously with 1 μM NaAsO2 for an additional 14 days and then harvested. Transcriptomic analysis of NaAsO2-treated progenitor-like HepaRG cells (Experiment 1 and Experiment 2) identified 743 and 639 differentially expressed genes, respectively, among which 343 genes were expressed in common. Pathway analysis of common differentially expressed genes demonstrated a substantial inhibition of cellular metabolic pathways, mainly lipid and xenobiotic metabolism, and cell death pathways. In contrast, cell proliferation, cell survival, and inflammation, were substantially activated. Treatment of differentiated HepaRG cells with NaAsO2 (Experiment 3) resulted in prominent gene expression changes, with a total of 1058 transcripts being significantly different from the control HepaRG cells. Pathway analysis of differentially expressed genes in NaAsO2-treated cells differentiated HepaRG cells showed activation of cellular death-associated pathways and inhibition of cell survival and cell proliferation.
Project description:The aim of this study was to measure the influence of beverages on blood gene expression. We wanted to explore the underlying mechanisms of the cardioprotective effects of red wine. Experiment Overall Design: Six healthy volunteers participated in this randomized controlled cross-over experiment. On 4 independent days they had 4 different beverages (500mL each: grape juice, red wine, 40g diluted ethanol, water). Blood samples were taken at baseline, 1, 2, 4, 12 hours after the drink together with standardized nutrition. RNA of 120 PBL samples was hybridized on Affymetrix microarrays. Three sources of variations were examined: individual, time and beverage.
Project description:RNA was sequenced from differentiated C2C12 mouse myotubes that were treated with S2-013 conditioned media with or without resveratrol in comparison to control media