Journal: BMC Cancer

Article Title: Overcoming acquired resistance to HSP90 inhibition by targeting JAK-STAT signalling in triple-negative breast cancer

doi: 10.1186/s12885-019-5295-z

Figure Lengend Snippet: Differential RNA expression in HSP90i-resistant clones compared to parental Hs578T cells. RNA samples from DMSO-treated and ganetespib-treated Hs578T, CR2 and CR3 cells were analysed for whole transcriptome profiling with RNA-sequencing. Differential gene expression analyses were performed between DMSO-treated parental Hs578T cells with either DMSO-treated CR2 or CR3 and the significantly upregulated genes observed in these clones were mostly overlapping. Pathway enrichment analysis using Metacore™ was performed on the significantly upregulated overlapping genes. The graph represents the top 20 most significantly upregulated pathways in the HSP90i-resistant clones, with FDR (false discovery rate) value < 0.05. Pathways highlighted in blue are linked to JAK-STAT signalling

Article Snippet: Duplicate samples (1 μg RNA in 30 μl) were subjected to RNA Sequencing (RNA-seq) analysis (Oxford Gene Technology) and gene expression was quantified using their analysis pipeline [ ].

Techniques: RNA Expression, Clone Assay, RNA Sequencing, Gene Expression

Journal: Cancers

Article Title: Common and Unique Transcription Signatures of YAP and TAZ in Gastric Cancer Cells

doi: 10.3390/cancers12123667

Figure Lengend Snippet: RNA-sequencing (RNA-seq) of the samples generated with gastric cancer MKN28 cells and activated mutants of YAP or TAZ genes. ( A ) Western blot analysis of YAP knockout (KO) and TAZ KO clones generated via the CRISPR/Cas9 system using two independent guide RNA sequences (labelled as 1 and 2) against human YAP and human TAZ. The wild type (WT) sample is shown in the first and last lane. β-actin is used as a loading control. The protein molecular weight size marker (unit: kDa) is depicted along the left of the Western blot images. The uncropped western blot figures in . ( B ) Representative immunofluorescence images of YAP and TAZ in WT, two clones of YAP KO and TAZ KO. ( C ) Western blot analysis of YAP KO cells transduced with empty vector (EV, control) or TAZ S89A (overexpression, OE). GAPDH is used as a loading control. ( D ) Western blot analysis of TAZ KO cells transduced with empty vector (EV) or YAP S127A (OE). β-actin is used as a loading control. The uncropped western blot figures in . ( E ) A schematic diagram of the samples prepared for RNA-seq.

Article Snippet: Quality check on the RNA samples, RNA-seq library preparation, sequencing, pre-processing and quantification of sequencing reads were done by AITbiotech (AITbiotech, Singapore, Singapore).

Techniques: RNA Sequencing, Generated, Western Blot, Knock-Out, Clone Assay, CRISPR, Control, Molecular Weight, Marker, Immunofluorescence, Transduction, Plasmid Preparation, Over Expression