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Pipeline publication

[…] ype control for 20 min before the addition to target cells. Cell suspensions were washed, stained for CD45-Pacific blue, CD3-PE and CD56-PE Cy7 (all from BioLegend) on ice in FACS buffer for 30 min, washed and briefly incubated with a 1 : 40 dilution of 7-AAD (BioLegend). Cells were measured on a FACS Canto II (BD Biosciences) and analyzed using FlowJo 9.3.2 software (Treestar)., To test whether the expression of miR-519a-3p, TRAIL-R2, CASP7 and CASP8 correlated with disease-free or relapse-free survival, the data sets GSE19783 (patients, n=101) and GSE22220 (patients, n=216) were downloaded from the NCBI GEO database (GEO Accession GSE19783 and GSE22220) and the meta-analysis data set from KM Plotter version 2016 (patients, n=3554) were used for human primary breast tumors. To test whether miR-519a-3p is differentially expressed in ER− and ER+ as well as wild-type and mutant TP53 data sets GSE19783 (patients, n=101) and GSE22220 (patients, n=216) were used, respectively. Correlations and statistical analyses were carried out using R packages ‘survival’ and ‘boxplot’ to generate Kaplan–Meier curves and boxplots. KM Plotter was used as an online tool. Log-rank and Student’s t-tests were performed. All P-values were calculated by means of a two-sided t-test where P-values of <0.05 were considered as significant, unless otherwise stated. Kaplan–Meier survival curves were carried out in GraphPad software (GraphPad software Inc., La Jolla, CA, USA). Enriched pathways predicted to be targeted by miR-519a-3p were identified using first the TargetScan (version 7.1) miRNA target prediction algorithm and then KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis within the functional enrichment tool DAVID Bioinformatics Resources (version 6.7) ()., We thank Dr. Aoife Ward and Dr. Aleksandra Balwierz for valuable discussions, and Ewald Münstermann, Sara Burmester, Julia Greiwe, Sabine Karolus, Angelika Wörner and Heike Wilhelm for excellent technical assistance. We thank the DKFZ Genomics and Proteomics Core Facility for performing cell line authentication and contamination control services. This work was supported by [email protected], the Deutsche Forschungsgemeinschaft (DFG DIP project WI3499/1-1) and the Baden-Württemberg Stiftung (BWST_NCRNA_035). NE was supported by the German Academic Exchange Service (DAAD)., Author contributions , CB conceived the project; CB, AB, AC and SW contributed […]

Pipeline specifications

Software tools KM plotter, TargetScan, DAVID