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Pipeline publication

[…] equences are listed in Supplementary Table ). An amount of 100 ng of purified PCR products was used as template for the indexed library preparation. We followed the Illumina TruSeq Nano DNA protocol, skipping the fragmentation step. After library validation and quantification (Agilent 2100 Bioanalyzer), equimolar amounts of library were pooled. Pools of 12 libraries were quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. Pools were sequenced using an Illumina HiSeq 4000 sequencer with a paired-end (76 × 7 × 76 cycles) protocol generating ~700 k reads/sample. The reads were aligned to the mouse GRCm38 reference with the Burrows-Wheeler Aligner (BWA 0.7.15) and the variants were called with the Genome Analysis ToolKit (GATK 3.7 Unified Genotyper) and annotated with Annovar (version 2016-02-01)., Results are presented as mean ± SEM, unless otherwise specified. Cohort sizes for in vivo experiments are noted in the respective figure captions. Cohort sizes were chosen based on experience gathered in previous experiments, . For the statistical analysis of survival data, log-rank tests were performed. For the statistical comparison of two independent groups, the unequal variances t-test (also known as Welch’s t-test, an adaption of Student’s t-test for unequal variances) was used, since variances between groups were generally not equal (F-test for equal variances). Statistical analyses, where values of the same individuals were compared pre- and post-treatme […]

Pipeline specifications

Software tools BWA, GATK, ANNOVAR
Organisms Mus musculus, Homo sapiens
Diseases Malnutrition, Leukemia, Lymphoproliferative Disorders, Leukemia, Lymphoproliferative Disorders, Substance-Related Disorders
Chemicals Hydrocarbons, Halogenated, Phosphoramides