Project description:In order to assess the effect of AGO2 on the transcriptional and post-transcriptional regulation of gene expression, RNA expression was profiled in untreated, CTRL siRNA transfected and AGO2 siRNA transfected HeLaS3 cells
Project description:We aimed to identify the effect of AGO2 depletion by genome editing on the mRNA expression profile of human cells. The experimental model used is the human cell line HeLaS3. All copies of AGO2 gene were disrupted by targeted genome editing using ZNF nucleases.
Project description:Characterization of AGO2 bound short RNAs from nuclear extracts of HeLaS3 cell line. Nuclei were isolated from HeLaS3 cells; a fraction of Nuclear lysates was harvsted and sequenced as the 'input' samples. The rest of nuclear lysates were Immunoprecipitated using AGO2 monoclonal antibodies or Isotype matched IgG. Following immunoprecipitation, RNA was extracted from AGO2 or control IgG IP for short RNA sequencing. Two independent biological replicates were carried out.
Project description:We knocked down AGO2 protein by RNAi in HeLaS3 human cell line. The current experiment aims at comparing nucleosome positioning in control and AGO2 knock down cells. HeLaS3 cell were cultured in DMEM. Cells were transfected with AGO2 siRNAs (or control siRNA) at day 1. On day 4 MNAse digestion of chromatin was performed. Mnase-digested chromatin DNA fragments were sequenced by paired-end DNA-seq.
Project description:In order to identify the effects of the knock-down of the gene of interest on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the knock-down cell line. Transcriptome analysis of the knock-down transgenic mouse ES cell line. The knock-down cell line (shE13) was generated by stably expressing a specific short-hairpin RNA against E13 sequence thus knocking-down E13 expression in parental mouse ES cell line E14Tg2a.4 (E14, Hooper M et al., 1987). The specific mouse gene knocked down in the ES cell line is E130012A19Rik.