GSM5034731: UNX_BMDM_Rep1; Mus musculus; RNA-Seq
Total RNA was purified using NucleoSpin RNA Isolation kit (Machery-Nagel, www.mn-net.com) according to the manufacturer's instructions. RNA quantity and quality were evaluated using NanoDrop and Bioanalyzer. RNA-Seq library preparation and sequencing were conducted using a NuGen universal plus mRNA-Seq kit. Sequencing was performed on Illumina NovaSEQ6000 system, using the paired-read 2x150 cycle option. RNA-Seq reads were generated using Illumina NovaSEQ6000 analysis pipeline. The read quality of all the samples were checked using FastQC v0.11.5. Adapter trimming, quality control, and base correction were performed by AfterQC (Chen et al., 2017). The sequencing reads in the FASTQ files of all the samples were aligned to the Mus musculus reference genome (Mus_musculus.GRCm38v91) with Spliced Transcripts Alignment to a Reference (STAR) version 2.6.0c. We next applied featureCounts v1.6.2 to assign reads to genes using mouse transcript annotations as a guide. EdgeR in R was used for data normalization and differential expression analysis of RNA-Seq expression profiles with biological replication. The Benjamini-Hochberg procedure was used to control the false discovery rate (FDR), and a cut-off criterion of FDR ≤ 0.05 was applied to identify differentially expressed genes. Individual gene expression was calculated as 'reads per kilobase per million mapped reads' (RPKM).
GEO Accession
GSM5034731