Computational protocol: SUMOylation of sPRDM16 promotes the progression of acute myeloid leukemia

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Protocol publication

[…] RNAs from the THP-1 cell line with stable expression of sPRDM16-WT or sPRDM16–K568R or a mock-transfected cell line were purified using TrizolTM method and subsequently cleaned using RNAeasy Kit (Qiagen). The polyadenylated RNAs purified from the cells were used for the construction of a sequencing library using the ScriptSeq Complete Gold Kit (Epicentre, Illumina). Cluster generation and sequencing were carried out using standard procedures in Hi-Seq 2500 Illumina platform. We used a single-end sequencing protocol to generate a 50 nt read at each end. RNA-seq reads were aligned to the human genome using TopHat (Johns Hopkins University, Baltimore, MD, USA). Cufflinks was employed to normalize Data and perform relevant comparisons among the different samples. Gene ontology analysis was performed using DAVID GO analysis software to search for enriched pathways. […]

Pipeline specifications

Software tools TopHat, Cufflinks, DAVID
Organisms Mus musculus
Diseases Leukemia, Myeloid, Acute