Project description:RNA-seq was performed on FACS-isolated stem cells from the mouse intestinal epithelium. The purpose of the experiment was to compare the transcriptomes of stem cells enriched for recently generated (young) mitochondria and stem cells enriched with old mitochondria. The dataset also includes samples of stem cells with young mitochondria deliberately contaminated with a small amount of Paneth cells, to control for accidental Paneth cell contamination in the sorting scheme.
Project description:Environmental stressors such as repeated social defeat may trigger powerful activation of sub-conscious parts of the brain. We examine the consequences of such stress in male rats on the pituitary gland. We prepared 20 Sprague Dawley rats. 10 of them were exposed to stress induced by the resident-intruder paradigm while the other 10 were controls. After dislocation of the neck under isoflurane anaesthesia, the pituitary gland was harvested. Total RNA was isolated from the tissues and used in mRNA sequencing.
Project description:Purpose: The goals of this study were to identify quantitative gene expression differences between wild type, Musashi1 null, Msuashi2 null and Musashi1/Musashi2 null MIAPaCa2 pancreatic cancer cells mRNA profiles of MIA PaCa-2 cancer cells were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.
Project description:Background: hnRNP K is an RNA-binding protein that's been implicated in oncogenesis, particularly in hematological disorders. Intent: To determine the impact of hnRNP K overexpression on RNA expression in murine fetal liver cells. Experimental Workflow: Fetal liver cells were subjected to retrovial transduction with either empty vector GFP or hnRNP K GFP. Purified GFP+ cells were flow sorted, and RNA was extracted from the GFP+ population, upon which RNA sequencing was performed.
Project description:Neuroblastoma (NB) is a pediatric cancer characterized by significant heterogeneity and poor prognosis, specially in high-risk cases with MYCN amplification. Understanding the molecular response of neuroblastoma to different treatments can provide insights into potential therapeutic strategies. The aim of this experiment as to asses in vivo response of combination of Prochlorperazine and Pitavastatin alone or along standard of care chemotherapy COJEC. Neuroblastoma in vivo model was obtained via subcutaneous injection of human high-risk, MYCN-amplified neuroblastoma organoids in NSG mice (PDX, LU-NB-1). When tumors reached 200-300 mm3, mice were randomized into treatment groups: control (n=7), PCZ + PIT combination (n=7), and PCZ + PIT combination + COJEC (n=6). PCZ + PIT (total volume 50 μl; 5 mg/kg of each drug) was administered i.t. daily five times per week. COJEC treatment was given i.p. and consisted of five different chemotherapies distributed in cycles over one week; Day 1 – cisplatin (1mg/kg) + vincristine (0,25mg/kg), Day 3 – etoposide (4mg/kg) + cyclophosphamide (75mg/kg), Day 5 – carboplatin (25mg/kg). All COJEC drugs were dissolved in saline and combination treatment was suspended in vehicle consisting of 2.5% DMSO, 2.5% Tween 80, 40% PEG, 55% PBS solution. Control mice were treated with i.t. injections of the vehicle used for PCZ+PIT and i.p injections of saline. Treatment was administered for 10 days, after which mice were euthanized, tumor pieces were collected snap-frozen. Mouse weights and tumor volumes were measured three times per week throughout the study. RNA was extracted from snap-frozen tumor pieces and RNA sequencing was conducted.
Project description:Neuroblastoma (NB) is a pediatric cancer characterized by significant heterogeneity and poor prognosis, especially in high-risk cases with MYCN amplification. Understanding the molecular response of neuroblastoma to different treatments can provide insights into potential therapeutic strategies. The aim of the experiment was to evaluate the effects of treatment of pitavastatin (PIT), prochloperazine (PCZ) and combination (PIT + PCZ) on LU-NB-2 PDX derived organoid model. In our experiments we observed synergistic effects on cell viability and cell death of those two compounds and further RNA-seq was intended to decipher effects of the combination on the neuroblastoma cells. Experimental Workflow: Sample Preparation: Tumor organoids were generated from PDX models of high-risk neuroblastoma patients with MYCN amplification. Treatment: LU-NB-2 PDX organoids were dissociated to single cells aseeded in T25 flasks, allowed to grow for 24 h, and treated for 48 h with the combination of PCZ +PIT (1.6 µM and 6.7 µM, n = 8), PCZ only (1.6 µM, n = 8), PIT only (6.7 µM, n = 8), or DMSO (n = 8). The treatment resulted in a ~15% decrease in NB cell viability in the combination group. RNA Extraction: Total RNA was extracted from the treated and control organoids. Library Preparation and Sequencing: RNA-seq libraries were prepared and sequenced to generate high-throughput sequencing data. Data Analysis: Differential gene expression analysis was performed to compare the treated samples against the untreated controls, aiming to elucidate the molecular effects of each treatment.
Project description:The histone variant H2A.B3 (H2A.Bbd/H2A.Lap1) has a tissue-specific expression pattern and is found to be most highly expressed during spermatogenesis. In order to investigate the role of H2A.B3 in chromatin packaging and regulation of spermatogenesis we created a line of TALEN-edited FVBN mice in which a deletion was introduced into the single exon of the H2AFB3 gene. The deletion was confirmed by Sanger sequencing and off-target effects investigated using exome sequencing. The deletion is visible in the RNA-Seq data of KO mouse, and the deleterious effect on the H2A.B3 protein has been confirmed using immunohistochemistry.
Project description:In mouse aorta endothelial cells, populations of endothelial vascular progenitor (EVP) and differentiated (D) cells could be identified by CD31 (lo/hi) and VEGFR2 (lo/hi) expression. These populations were FACS sorted and paired-end bulk RNA-sequencing was performed.
Project description:Affymetrix Human Gene 1.1 ST Array profiling of 285 primary medulloblastoma samples. Total RNA was extracted from primary medulloblastoma samples and hybridized to Affymetrix Human Gene 1.1 ST Arrays (24-Array Plates) according to the manufacturer's instructions.