Project description:Interventions: lesion tissues vs. adjacent tissues of colorectal cancer patients:nil
Primary outcome(s): RNA
Study Design: Factorial
Project description:<p>We used massively parallel, paired-end sequencing of expressed transcripts (RNA-seq) to detect novel gene fusions in short-term cultures of glioma stem-like cells freshly isolated from nine patients carrying primary glioblastoma multiforme (GBM). The culture of primary GBM tumors under serum-free conditions selects cells that retain phenotypes and genotypes closely mirroring primary tumor profiles as compared to serum-cultured glioma cell lines that have largely lost their developmental identities.</p>
Project description:Antisense and sense probes of noncoding RNA GAS5 were used to perform the RNA pull down experiment on mouse hippocampus tissues. Then the proteins were identified by LC-MS/MS.
Project description:Healthy hearts from warm cadavers not usable for heart transplants were identified and tissues were isolated from these. From ventricle tissues, cardiomyocytes were further isolated. Bulk-RNA-sequencing was performed.
Project description:single cell RNA sequencing of freshly isolated mouse BFU-E (burst forming unit-erythroid ) cells cultured for 1, 2, or 3 days with and without 100nM dexamethasone
Project description:Freshly dissected Thymus, Kidney, and Spleen from young and aged mice were subjected to collagenase digestion to prepare single-cell suspension for the isolation of endothelial cells. Endothelial cells form the single-cell suspension was isolated using a magnetic bead-based separation method using CD144 and Endomucin antibody. RNA from 150,000 cells from each group was isolated using the RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s instructions. The library preparation was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina.
Project description:Purpose: The goal of this study was to characterize molecular stress responses on transcriptional level in dorsal and ventral hippocampus separately. Methods: mRNA profiles of whole, dorsal and ventral hippocampus of mice 45min after first exposure to different acute stressors. The stressors were novelty (6min novel environment), restraint (30min immobilization), or cold swim (6min in 18 degree Celcius water). 5 mice were used per condition, using Illumina HiSeq4000. The sequence reads that passed quality filters were mapped with STAR, counted with RSEM and differential gene expression was calculated using the bioconducter package edgeR. Results: With our workflow, we identified 13902 genes per sample. Approximately 20% of the genes were differentially expressed between dorsal and ventral hippocampus at baseline, with a log2 fold change >±0.3 and p value <0.005. Approximately 100 genes are differentially expressed upon stress treatment in the whole hippocampus. If ventral and dorsal hippocampus were analyzed separately, numbers increased to 150 and 250 respectively. Stress-responsive genes vary between dorsal and ventral hippocampus, and also vary between different stressors. Further analysis identified a functional epigenetic gene cluster specific for the stress response in the ventral hippocampus. Conclusions: Our study represents the first RNA-seq analysis of dorsal and ventral hippocampus after different acute stress exposures.
