Project description:RNA-seq on K562 cells treated with a CRISPR gRNA against STAU2. (STAU2-BGKcLV11) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:PTBP1 is a widely expressed RNA binding protein known to play roles in regulation of alternative pre-mRNA splicing and other post-transcriptional processes. The PTBP2 paralog is expressed in neurons and switching from expression of PTBP1 to PTBP2 regulates a subset of alternative splicing events during neuronal differentiation. The PTBP3 paralog is conserved across vertebrates and is expressed highly in cells of the hematopoietic system. However, the unique non-redundant roles of PTBP3 are currently unclear. We therefore tested the transcriptomic consequences of knocking down PTBP3 in human K562 erythroleukemia cells. K562 cells were treated with two separate siRNAs (Rd5 and Rd9) targeted against all isoforms of PTBP3 or with a control non-specific siRNA (C2). Triplicate samples were used for each of the three experimental conditions. Transcriptome analysis used the Affymetrix HJAY array, allowing detection of changes in alternative splicing and in transcript levels. Despite at least 75% PTBP3 depletion, as monitored by western blot, only modest changes at the transcriptome level were observed.
Project description:The double-stranded RNA binding protein Staufen2 (Stau2) is asymmetrically localized and segregated during asymmetric cell divisions in the developing mouse cortex and promotes intermediate progenitor cell fate. We carry out RNA immunoprecipitation with a Stau2 specific antibody, followed by microarray analysis to identify Stau2 assoicated RNAs that may be shuttled asymmetrically into one daughter cell thus affecting cell fate. Cortex was dissected from E13-14 timed-pregnant Swiss Webster Mice (Taconic) and RNA immunoprecipitation followed by microarray analysis was carried out to identy Stau2 associated RNA cargos.
Project description:The double-stranded RNA binding protein Staufen2 (Stau2) is asymmetrically localized and segregated during asymmetric cell divisions in the developing mouse cortex and promotes intermediate progenitor cell fate. We carry out RNA immunoprecipitation with a Stau2 specific antibody, followed by microarray analysis to identify Stau2 assoicated RNAs that may be shuttled asymmetrically into one daughter cell thus affecting cell fate.
Project description:microRNA profiling of human K562 cells comparing control or ETO2-overexpressed cells Two-condition experiment, K562-pcDNA vs. K562-pcDNA-ETO2, Biological replicates: 1, 1 pcDNA, 1 pcDNA-ETO2, independently.
