Computational protocol: Widespread changes in transcriptome profile of human mesenchymal stem cells induced by two-dimensional nanosilicates

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Protocol publication

[…] hMSCs were treated with and without nanosilicates (50 µg/mL) for 48 h; nanosilicates were then removed and cells were cultured under normal conditions for an additional 5 d. Samples were analyzed via a high-output HiSeq platform with TruSeqRNA sample preparation and single-end read length of 125 bases. The sequenced reads were trimmed and aligned to the human genome (hg19). GLMs were used to identify the differentially expressed genes where the expression counts were modeled as negative binomial distribution. Only genes with a P adjusted value (false-discovery rate) of less than 0.05 were included within the network and subsequent GO term network formation. Data were analyzed using Cytoscape, GeneMANIA, ClueGO, and DAVID bioinformatics resources. […]

Pipeline specifications

Software tools GeneMANIA, ClueGO, DAVID
Application RNA-seq analysis
Organisms Homo sapiens
Diseases Carcinoma, Transitional Cell
Chemicals Graphite