Project description:This study used Drosophila melanogaster S2 cells treated with siRNA against the EJC components mago or eIF4A3, or a non-targeting control siRNA (three samples per condition). mRNA-seq libraries were prepared from the samples and the data was used to examine 'RS-exons' - exons which reconstitute a 5' splice site when they are spliced to the upstream exon. In contrast to mammalian cells, RS-exons are not recursively spliced out from Drosophila transcripts after perturbation of the EJC.
Project description:RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF4A3. (EIF4A3-BGHcLV16) 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:RNA-seq on K562 cells treated with a CRISPR gRNA against EIF4A3. (EIF4A3-BGKcLV15) 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:COP1 regulates MAP kinase dependent stability Pea3 transcription factors. We determined the role of COP1 in the regulation of MAP kianse transciptional output. We transfected GIST882 cells with siRNA against a scrambled sequence and two sequences against COP1. We treated cells for 8 hours with vehicle or 100 nM PD0325901 in duplicate and isolated RNA for sequencing.
Project description:We performed ChIP-seq targeting the glucocorticoid receptor (GR) in the U2OS-GR cell line. The cell line is derived from U2OS ATTC:HTB-96 and stably transfected with an expression construct for rat GR. The cells were treated with 100 nM dexamethasone for 4 hours, washed 2x with PBS and cultured in hormone-free medium for 24 hours before harvest.
Project description:Nonsense-mediated mRNA decay (NMD) can occur independently of some NMD factors such as UPF3B. We have performed total RNA-Seq in HCT116 cells under NMD factor knockout (with CRISPR-Cas9) and/or knockdown (with siRNA transfection) conditions to identify mRNA substrates regulated by different NMD factors. We have also performed RIPiT-Seq to identify the footprints of three compositionally distinct EJCs that contain the following pairs of proteins: MAGOH-EIF4A3, UPF3B-EIF4A3 or CASC3-EIF4A3 in WT HCT116 cells.
