Computational protocol: Potential Biomarkers for Radiation-Induced Renal Toxicity following 177Lu-Octreotate Administration in Mice

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Protocol publication

[…] Genome-wide transcriptional analysis and data processing has been previously described [, ].Homogenization of the tissue samples was performed with the Mikro-Dismembrator S ball mill (Sartorius Stedim Biotech) and total RNA extraction was performed with the RNeasy Lipid Tissue Mini Kit (Qiagen), according to the instructions of the manufacturer. The quality assessment of the samples was conducted through the NanoDrop ND-1000 and the RNA 6000 Nano LabChip Kit with Agilent 2100 Bioanalyzer (Agilent Technologies), with a RIN cut-off value of 6.The RNA samples were processed at SCIBLU (Swegene Center for Integrative Biology at Lund University) using MouseRef-8 Whole-Genome Expression Beadchips (Illumina). The image acquisition and analysis were performed with the Illumina BeadArray Reader scanner and BeadScan, respectively.The web-based BioArray Software Environment (BASE) was used for data preprocessing and quantile normalization. Nexus Expression 3.0 (BioDiscovery, El Segundo, CA, USA) was used for further data analysis using log2-transformed, normalized expression values, and variance filter. Differential expression was determined using the Benjamini-Hochberg method to control the false discovery (FDR-corrected P value < 0.01). A log2-ratio > 0.58 were considered significant. Generated transcriptional profiles are available from the NCBI’s Gene Expression Omnibus (GEO accession number GSE54674).Further analysis, including up-stream regulators and pathway analysis, was conducted using the IPA software (Ingenuity Systems, Redwood City, USA). […]

Pipeline specifications

Software tools BASE, Nexus Expression
Application WGS analysis
Organisms Mus musculus
Diseases Kidney Diseases
Chemicals Succimer, Urea, Technetium Tc 99m Dimercaptosuccinic Acid