GSM8521408: FR0797-CC-VC; Homo sapiens; RNA-Seq
Total RNA was extracted from pediatric AML cells following coculture with pediatric mesenchymal stem cells (pMSCs) using standard RNA isolation techniques. RNA was prepared for downstream RNA sequencing (RNA-seq) analysis to assess transcriptional changes due to coculture conditions. Quality of sequencing was assessed using FastQC version 0.11.5 (Andrews, 2010), and sequences were trimmed using TrimGalore version 0.4.4_dev (Krueger, 2015) with 3' end trimming and paired parameters, using a quality score threshold of 20. The reference genome (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz) was obtained via Ensembl (http://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/, 11/01/2018); reads were aligned to the genome using hisat2 (Kim et al. 2015).