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

Journal: American Journal of Cancer Research

Article Title: Chk1 inhibitor-induced DNA damage increases BFL1 and decreases BIM but does not protect human cancer cell lines from Chk1 inhibitor-induced apoptosis

doi:

Figure Lengend Snippet: Inhibition of Chk1 increases BFL1 and decreases BIM expression in U2OS cells. (A) HT29 or U2OS cells were treated with 1x γH2AX EC50 of V158411 for 24 hours (γH2AX EC50 values from [12]) and gene expression determined by RNAseq analysis. Values are the mean of 2 independent replicates. (B) U2OS cells were treated with 3x GI50 of V158411 for 24 hours (GI50 values from [12]) and BCL2A1 (BFL1) mRNA expression determined using ViewRNA technology. Each point represents an individual cell. Data is derived from 3 independent wells. Significance was determined by Student’s t-test (***P < 0.001). U2OS cells were treated with (C) 3x GI50 for the indicated times, (D) 3x GI50 for 1-48 hours or (E) 0.1-3x GI50 for 48 hours and protein expression determined by western blotting.

Article Snippet: RNAseq expression analysis RNAseq analysis was conducted by Lexogen (Vienna, Austria).

Techniques: Inhibition, Expressing, Gene Expression, Derivative Assay, Western Blot

Journal: Genome Medicine

Article Title: Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes

doi: 10.1186/s13073-021-00952-5

Figure Lengend Snippet: Ability of a k-nearest neighbour classifier to predict subtype of ovarian cancer cell lines. A Metagene signatures for which high expression is informative of each cluster were extracted using gene scoring scheme as per Kim and Park . Colours represent the strength of the association between that gene and the cluster, where red indicates the strongest association. The top track indicates cluster number, as per Fig. . B Evaluation of three machine learning algorithms for OC cell line subtype classification: k-nearest neighbour (KNN), random forest (RF) and support vector machine (SVM). Cell lines were designated the subtype indicated by NMF clustering and partitioned into 4 subsets. Three subsets were used to train each of the machine learning algorithms, with the fourth set held out as a test set. The four subsets were rotated such that each sample had the opportunity to be trained and tested upon. The average per-class sensitivity and specificity score across the four tested sets are shown. Balanced accuracy scores for HGSOC were 1 (KNN), 0.935275 (RF) and 0.984375 (SVM), and the overall kappa values for each model are 0.918 (KNN), 0.78905 (RF) and 0.878 (SVM). C Principal component analysis of patient-derived OCMs. Colours indicate the subtype determined by a pathologist. D Comparison of the identified subtype based upon pathology, and the k-nearest neighbour (KNN), random forest (RF) and support vector machine models trained in B deployed on the OCMs. E Closer inspection of the performance of the RF model. Pathology and RF-predicted subtype are indicated above the heatmap. HGSOC cell line Kuramochi is included in parts C – D as a positive control. The models are referred to using the OCM prefix followed by the patient number and, if one of a series, the biopsy number. + EpCAM positive; − EpCAM negative; P4 and P14 indicate passage number of this OCM; NOS, not otherwise specified

Article Snippet: Kuramochi cells for analysis by RNAseq (JCRB Cell Bank) were cultured in RPMI supplemented with 5% FCS, 100 U/ml penicillin, 100 U/ml streptomycin and 2 mM glutamine and were maintained at 37°C in a humidified 5% CO 2 atmosphere.

Techniques: Expressing, Plasmid Preparation, Derivative Assay, Comparison, Positive Control