Following quality assessment by Nanodrop spectrophotometry®, this was hybridised to a commercially available targeted Oligo-GEArray® gene filter, Human Inflammatory Cytokines and Receptors (OHS-011, Superarray Bioscience, USA), representing 112 inflammatory cytokine and receptor genes.
Cerebellum samples were sequenced using Illumina Genome Analyzers with modifications for mRNA samples [39], [42], [43], [52], [57]: Following quality assessment using a Bioanalyzer 2100 (Agilent Inc., Santa Clara, CA; Table 1), poly A+ RNA was isolated from 5 10 µg total RNA by two rounds of oligo-dT selection (Invitrogen Inc., Santa Clara, CA).
Following quality assessment using a Bioanalyzer 2100, single-stranded cDNA-adapter fragments were randomly annealed to the surface of a flow cell in a cluster station (Illumina Inc., San Diego, CA) via primers complementary to the adapters and incubated under conditions fostering annealing of the ends of cDNA-adapter fragments to adjacent complementary primers.
Following quality assessment, poly (A) mRNA preparation and sequencing with an Illumina HiSeq 1000 sequencer (Illumina Inc., San Diego, CA, USA) were performed as described previously [ 52].
Total RNA from the slm/ml and the rest of the CA1 were extracted with the miRVana isolation kit (Ambion, Austin, TX, USA) and quantified with a NanoDrop ND-1000 spectrophotometer, followed by quality assessment with the 2100 Bioanalyzer (Agilent Technologies), according to the manufacturer's instructions.
Following these quality assessment interventions, we expect an error of approximately 11% in the information considered relevant to the analysis.
Total RNA was quantified with a NanoDrop ND-1000 spectrophotometer followed by quality assessment with the 2100 Bioanalyzer (Agilent Technologies) according to the manufacturer's instructions.
Following strict quality assessment procedures in both techniques, (RNA quality, cross-hybridisation of microarray probes, microarray spot intensity, qPCR primer design, and PCR efficiency) and data filtering after normalization (cut-offs for fold-changes and low microarray spot intensity) resulted in high correlation between qPCR and microarray data (Additional file 9) [ 60, 61].
The articles were independently screened based on inclusion and exclusion criteria, followed by a quality assessment of all included articles.
Patient Intervention Comparator Outcome Study type (PICOS) [ 33] criteria were followed and the quality assessment was performed according to the NICE checklist for RCTs [ 34].
Illumina sequencing data was converted to FASTQ format using Casava pipeline followed by read quality assessment using FASTQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).ac.uk/projects/fastqc/
