title: Illumina HiSeq 2500 paired end sequencing; RNAseq of human cell line RPCI-WM1 comparing artificial PRDM1-targeting miRNA to non-targeting control, and comparing Tazemetostat treatment to DMSO. ChIPseq for the factors BLIMP1 and H3K27me3 in the RPCI-WM1, OPM-2 and NCI-H929 cell lines, along with ChIPseq for EZH2 in the NCI-H929 cell line.
design: RNAseq of human cell line RPCI-WM1 comparing artificial PRDM1-targeting miRNA to non-targeting control, and comparing Tazemetostat treatment to DMSO. ChIPseq for the factors BLIMP1 and H3K27me3 in the RPCI-WM1, OPM-2 and NCI-H929 cell lines, along with ChIPseq for EZH2 in the NCI-H929 cell line.
library_construction_protocol: Cells were harvested from culture, washed in PBS. The cells with inducible artificial miRNAs were treated with 0.2µg/mL doxycycline for 48h. RNA was extracted using TRI reagent ((#AM9738, Thermo Fisher Scientific) according to the manufacturer's protocol, , then treated with HL-dsDNase (#70800-201, ArcticZymes). RNA was then purified using the RNeasy MinElute Cleanup Kit (#74204, Qiagen), and assessed for quality and quantity using the RNA 6000 Nano kit (#50671511, Agilent) with the 2100 Bioanalyzer Instrument. RNAseq libraries were constructed using the NEB NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (#E7420S, New England Biolabs) in combination with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490S, New England Biolabs).
attributes.tag: Experimental Factor: RNA interference
attributes.value: PRDM1-miR