Transcription profiling of migratory vs sedentary brown trout (Salmo trutta) and wild vs hatchery Atlantic salmon (Salmo salar)
Ontology highlight
ABSTRACT: A total of 55 individuals were analysed: 15 migratory brown trout (Salmo trutta) individuals from the Redon river, 15 sedentary brown trout (S. trutta) individuals from the Redon river, 15 sedentary brown trout (S. trutta) individuals from the Chevenne river, and 10 Atlantic salmon (S. salar) individuals of a hatchery strain. For each individual, RNA was isolated twice from different parts of the same tissue, independently reverse transcribed into Cy3-labeled cDNA and then probed on two different slides, which leads to total of 110 single slide experiments.
Project description:The main purpose of the experiment is to look for changes in the transcriptome of LNCaP cells during neuroendocrine differentiation induced by incubation in steroid stripped serum (charcoal treated fetal bovine serum) for four days.
Project description:This set of 320 profiles was utilized to construct, validate and evaluate a gene-expression based classifier of outcome of neuroblastoma patients
Project description:RNA splicing and protein degradation systems allow functional adaptation of the proteome in response to changing cellular contexts. However, the regulatory mechanisms connecting these processes remain poorly understood. Here, we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic 5′ splice sites. Importantly, disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing proteotoxic aggregates, ER stress and CHOP-mediated cell death. In response to impaired splicing, eukaryotic cells enhance ubiquitination and ER-phagy to alleviate the pathogenic translation of proteotoxic exons. Our findings show how cryptic splicing-inducedproteotoxicity can be mitigated, and provide insight into the molecular pathogenesis of spliceosome-associated diseases, such as retinitis pigmentosa.
Project description:To identify epigenetically silenced genes in multiple myeloma (MM) cell lines and to determine the effects of 5-aza-2-deoxycytidine and trichostatin A on gene expression. We treated 3 multiple myeloma cell lines (MM1, NCI-H929, U266) with 5-aza-2-deoxycytidine and/or trichostatin A.
Project description:To investigate mechanisms of metal tolerance in the gill, gut, kidney and liver of brown trout inhabiting the river Hayle (highly metal contaminated) compared with a control population from the river Teign.
Project description:To investigate mechanisms of metal tolerance in the gill, gut, kidney and liver of brown trout inhabiting the river Hayle (highly metal contaminated) compared with a control population from the river Teign. mRNA samples were sequenced (Illumina GAII) from a pooled embryonic sample and 12 multiplexed samples of different tissues from the the Hayle and Teign populations (pooled from 5 and 10 individuals respectively) and used to generate a transcriptome assembly. Expression profiling was then conducted for the gill, gut, kidney and liver samples. Expression profiling results are presented in this Series.
Project description:1. effect of radiation on transcription in normal and radiation sensitive primary human fibroblasts. 2. comparison of the basal transcription levels in normal and radiation sensitive primary human fibroblasts.
Project description:Integrative proteo-trnascriptomics analysis of MDR abd drug sensitive E. coli strains isolated from river Yamuna, Delhi, India to identify novel drug targets against Multi drug Resistant E. coli
Project description:Investigation of transcriptome variability in neurospheres originating from separate isolations (individuals), different passages and parallel cultures. As a control neurospheres were also compared to neurospheres induced to differentiate by adding serum and plating onto solid support.
Project description:To elucidate the mechanisms underlying the perturbation of tumor vascularization in Pparb/ mice we performed matrigel plug assays23. Matrigel containing prostaglandin E2 (PGE2) and basic fibroblast growth factor (FGF-2) was injected subcutaneously into both wild-type and Pparb/ mice where it formed semi-solid plugs. These plugs became rapidly invaded by AQP-1 positive cells. To analyze differences between Pparb+/+ and Pparb/ samples we compare the gene expression profile of both samples by microarray analysis.