Similar protocols

Pipeline publication

[…] cipitates and their supernatants were analyzed by immunoblotting., Mean values were derived from at least three experiments. Depending on the number of groups examined, comparisons were carried out using either Student’s t-test (two groups) or one-Way ANOVA and Bonferroni post-hoc analysis (more than two groups). Significance was defined as P < 0.05. Statistical analysis was performed using the SPSS software (Release 10.0.1, SPSS, Chicago, IL, USA)., 17 samples from 9 AD patient and 8 control post-mortem brain samples, subjected to NGS expression analyses and nELAVL HITS-CLIP, were retrieved from GEO repository (accession number GSE53699). Raw Seq data were initially quality checked with FastQC and further processed for adapter removal with a combined use of Minion and Trimgalore. Following pre-processing, quantification of expression at gene and at transcript level was performed using Kallisto. GRCh38 and Ensembl 81 were utilized as reference genomes and transcriptomes, respectively. All downstream analyses were implemented using R/Bioconductor. The data had an average of 60 million PE reads. Initial standard differential expression analysis revealed that samples exhibited high heterogeneity, even within the same group. We found that this high level of intra-group variance diminished the number of differentially expressed transcripts between control and AD samples, an observation that was also noted by the authors of the original manuscript. Subsequently, APP isoform levels were normalized against APP gene expression in each sample. Associations between normalized APP iso […]

Pipeline specifications

Software tools FastQC, Trim Galore!, kallisto