The long non-coding RNA ELDR suppresses tumorigenicity of AML cell lines with MLL rearrangements by interfering with DNA replication and chromatin accessibility [RNA-Seq]
RNA-seq analysis comparing the transcription of stable ELDR overexpressing THP-1 lines (C1 and C3) with empty vector (EV) controls. Overall design: RNA was extracted using RNeasy Mini Kit (Qiagen) and RNA libraries were prepared from 900ng of total RNA previously checked for integrity (RIN above 9.5). Ribodepletion and library preparation were performed with Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research). Library size distribution was assessed on a 2100 bioanalyzer (Agilent Technologies) and libraries were quantified by qPCR. Equimolar libraries were sequenced in paired end reads (PE50) on a Novaseq 6000 system (Illumina), with a NovaSeq S1 flow cell and a coverage of 50M fragments per library. Sequencing reads were aligned to the GRCh38 genome using STAR v2.7.9a . The raw counts were calculated with FeatureCounts v2.0.3 based on the human reference genome (release 102).DESeq2 R package was used to compute FPKM values and logFC.A genome coverage file was generated and scaled to RPM using Bedtools.