mRNA-seq and AGO2-RIP-seq of JURKAT T-cell acute lymphoblastic leukemia cell line upon overexpression of hsa-miR-143-3p

The aim of this study was to investigate the effect of hsa-miR-143-3p on global gene expression in T-cell acute lymphoblastic leukemia (T-ALL) and to unravel its direct target genes. For this purpose we selected Jurkat T-ALL cell line characterized by low expression of this miRNA. The cells were transduced either with pCDH-CMV-MCS-EF1_GFP_puro empty vector (System Biosciences) or pCDH-CMV-MCS-EF1_GFP pre-mir-143 vector, each variant in three biological replicates. Total RNA was isolated from each samples. Additionally, RISC complexes containing miRNAs bound to their target mRNAs were isolated by AGO2 immunoprecipitation and the obtained fraction of RISC-bound RNA was isolated from each sample. All 12 libraries (6 total RNA samples and 6 AGO2-RIP samples) were sequenced on Illumina NovaSeq6000 platform, in 2x150 mode, with a coverage of 60M paired reads/sample.

本研究旨在探究hsa-miR-143-3p对T细胞急性淋巴细胞白血病（T-cell acute lymphoblastic leukemia, T-ALL）中全基因组基因表达的影响，并解析其直接靶基因。为此，我们选取了该miRNA表达水平较低的Jurkat T-ALL细胞系作为实验材料。将细胞分别转导至pCDH-CMV-MCS-EF1_GFP_puro空载体（System Biosciences公司）或pCDH-CMV-MCS-EF1_GFP pre-mir-143载体中，每组设置3次生物学重复。随后从每份样本中提取总RNA。此外，通过AGO2免疫沉淀法分离结合了miRNA及其靶mRNA的RNA诱导沉默复合体（RNA-induced silencing complex, RISC），并从每份样本中获取结合RISC的RNA组分。最终，所有12个测序文库（6个总RNA样本与6个AGO2-RIP样本）均在Illumina NovaSeq6000测序平台上以2×150 bp双端测序模式进行测序，每个样本的双端读段覆盖度达60M。