Pipeline publication

[…] 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 prim […]

Pipeline specifications

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