Computational protocol: Prevention of diabetes in overweight/obese children through a family based intervention program including supervised exercise (PREDIKID project): study protocol for a randomized controlled trial

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Protocol publication

[…] Eligible participants will be randomly assigned after completing the baseline measurements to either the control group or the or exercise group (Fig. ). Randomization of the participants into the control or exercise group will be done using Statistical Package for Social Sciences (IBM SPSS Statistics for Windows, version 21, Armonk, NY, USA) by an independent researcher. Assessment staff will be blinded to participant randomization assignment. Participants and their parents or guardians will be explicitly informed of the group to which they will be assigned, as well as of the study hypotheses. As exercise is potentially beneficial for the health of the children recruited in this trial, the waiting list control group strategy will be used, which means that the control group will receive the same exercise program when the post-intervention evaluations are finished.Fig. 2 [...] Species of miRNA present on samples of individual subjects, before and after the intervention program, will be analyzed using RNA-seq methodology on Illumina’s MiSeq Next Generation Sequencing system. This workflow allows one to fully characterize the miRNA profile present in the samples analyzed (exosomes and white blood cells) and to quantify the expression levels of different miRNA species. In this sense, effects of the intervention program on the miRNA profile and on expression level of specific species can be inferred. Briefly, Illumina’s TruSeq Small RNA Sample preparation kit will be used to generate sequencing libraries, from 1 μg of total RNA isolated from previous samples (either exosomes or white blood cells). Only 145 to 160 bp libraries will be selected for sequencing, as they include miRNA species (22–30 bp plus adapters). Sequencing reactions will be performed on Illumina’s MiSeq Reagent Kit V3, which supports to multiplex up to 10 samples on a single run, and single reads of 50 nt in length. Analysis of results, FASTQ files generation and sequence alignment will be performed using specific software packages (MiSeq Reporter, Bowtie, SAMtools, DESeq2 and miRDeep). […]

Pipeline specifications

Software tools SPSS, Bowtie, SAMtools, DESeq2
Applications Miscellaneous, RNA-seq analysis
Organisms Homo sapiens, Dipturus trachyderma
Diseases Diabetes Mellitus, Diabetes Mellitus, Type 2, Insulin Resistance
Chemicals Glucose