Pipeline publication

[…] A) with accession number PRJEB23139 as primary accession number and ERP104872 as secondary accession number. https://www.ebi.ac.uk/ena/data/view/PRJEB23139., Fold change of differentially regulated genes and their adjusted p-values were depicted using volcano plot using the R package., The pathway plot was analyzed via iPathway Guide using impact analysis that looks at over-representation of differentially expressed genes in a given pathway and the total gene accumulation in a given pathway. The underlying pathway topologies, comprised of genes and their directional interactions, are obtained from the KEGG database., The hierarchical clustering and Venn plot were carried out using rpudplus, hclust and Venn diagram function in R-Studio employing differentially expressed pre-ranked genes which were associated with extracellular secretory function as classified using TopGO R-Studio package and GeneTrail2. The principle component analysis (PCA) based on regularized log transformed FPKM values with an adjusted p-value < 0.05. obtained from DEseq. 2 and was carried out using ggfortify and ggplot2 packages in R-Studio. (R Tutorial with Bayesian Statistics Using OpenBUGS, Chi Yau, ASIN: B006ZP4SKW)., To validate the RNA-Seq data, we performed qRT-PCR of selected genes enrolling MSCs treated with S100A8/A9 for 6 and 24 h, respectively as opposed to untreated MSCs. RNA was isolated as described above. The AD-MSC were subjected to M-MLV reverse transcriptase RNase H Minus (Promega, #M3681) and Oligo dT primers 0.5 µg/µl (Promega, #C1101) to generate complementary DNA and the miRNA cDNA was transcribed using miScript II RT kit (Qiagen, Cat # 218160), that was diluted to 4 ng RNA/well. The cDNA was further amplified with gene-specific […]

Pipeline specifications

Software tools Hclust, TopGO, GeneTrail, DESeq
Organisms Mus musculus
Diseases Inflammation
Chemicals Calcium, Metals, Alkaline Earth