Computational protocol: All-trans retinoic acid and arsenic trioxide fail to derepress the monocytic differentiation driver Irf8 in acute promyelocytic leukemia cells

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Protocol publication

[…] Raw sequence reads were initially processed using FastQC (Babraham Institute, Cambridge, UK) for quality control, and then adapter sequences and poor quality reads were removed using Cutadapt. Quality-filtered reads were then mapped to mm9 using STAR, and only uniquely mapped reads were kept. Read counts were calculated using HTSeq-count. Differentially expressed genes were identified using R package DESeq2 (P<0.05, fold change >1.5). All the RNA-seq raw data have been deposited in GEO database under the accession numbers GSE46434 and GSE94017. […]

Pipeline specifications

Software tools FastQC, cutadapt, STAR, HTSeq, DESeq2
Application RNA-seq analysis
Organisms Homo sapiens
Diseases Leukemia, Promyelocytic, Acute
Chemicals Tretinoin