Journal: The Journal of Biological Chemistry

Article Title: Transcription factor SOX15 regulates stem cell pluripotency and promotes neural fate during differentiation by activating the neurogenic gene Hes5

doi: 10.1016/j.jbc.2023.102996

Figure Lengend Snippet: Gene expression profile of Sox15 -knockout ESCs . A , RNA-seq analysis identifies differentially expressed genes (DEGs) in Sox15 KO1 ESCs compared to WT, plotted as a function of mean expression (fpkm) and fold changes (log2). Number of genes upregulated (830) and downregulated (589) are indicated. B , gene ontology (GO) analysis on DEGs in Sox15 KO1 ESCs compared with all annotated genes. p -value per GO classification is shown (-log10( p -value)). C , heatmap showing the relative expression levels of indicated genes from three biological replicates each of WT and Sox15 KO ESCs. Scaled values indicate relative downregulation ( red ) or upregulation ( green ) of gene expression. Genes from each category are manually curated. ESC, embryonic stem cell.

Article Snippet: RNA-seq samples were processed using the RNA-seq pipeline implemented in bcbio-nextgen v1.1.3 ( https://bcbio-nextgen.readthedocs.org ).

Techniques: Expressing, Knock-Out, RNA Sequencing Assay

Journal: Scientific Reports

Article Title: Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts

doi: 10.1038/s41598-019-42680-2

Figure Lengend Snippet: Illustration of bioinformatics strategy and workflows for analyzing patient- and PDX-RNAseq. ( a ) Bioinformatics strategy to separate mouse-stroma and human-tumor expression levels from PDX RNAseq data; ( b ) Dotted box indicates patient and PDX Pipelines for processing donor tumors and PDX tumors, respectively; ( c ) Dotted box indicates workflow for examining technical and biological differences.

Article Snippet: A PDX RNAseq analysis pipeline was devised based on Xenome and a standard patient tumor pipeline (Fig. ).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts

doi: 10.1038/s41598-019-42680-2

Figure Lengend Snippet: Identification of genes sensitive to patient- versus PDX-RNAseq bioinformatics pipelines. Nine patient donor tumors were processed through patient- and PDX-RNAseq piplines separately; differential expressed genes (DEGs) between the two pipelines are used to determine genes sensitive to pipeline differences. ( a ) MA (M: log ratio, A: Mean average) plot with DEGs highlighted in red; ( b ) Distribution of phast conservation score for all genes and DEGs caused by pipeline differences.

Article Snippet: A PDX RNAseq analysis pipeline was devised based on Xenome and a standard patient tumor pipeline (Fig. ).

Techniques:

Journal: Scientific Reports

Article Title: Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts

doi: 10.1038/s41598-019-42680-2

Figure Lengend Snippet: Expression differences of donor-PDX tumor pairs and impact on transcriptome pair similarity. RNASeq for nine pairs of donor/PDX tumors were processed with patient and PDX pipelines respectively. XDGs indicate differentially expressed genes between paired donor/PDX tumors after excluding previously identified genes that are sensitive to pipeline differences. ( a ) MA plot with XDGs in red; ( b ) Box plot of correlation coefficients of paired PDX-donor tumors before and after removing XDGs; ( c ) Hierarchical clustering of donor/PDX tumor pairs before removing XDGs; ( d ) Hierarchical clustering of donor/PDX tumor pairs after removing XDGs. Patient hetrotransplant (PH) numbers represent a single tumor line and the suffix indicates either the patient donor (P) or corresponding xenograft (PDX).

Article Snippet: A PDX RNAseq analysis pipeline was devised based on Xenome and a standard patient tumor pipeline (Fig. ).

Techniques: Expressing