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: bioRxiv

Article Title: RNAseq analysis of rodent spaceflight experiments is confounded by sample collection techniques

doi: 10.1101/2020.07.18.209775

Figure Lengend Snippet: Liver and quadriceps samples were dissected from mice immediately after euthanasia with pentobarbital/phenytoin (Euthasol ® ) then preserved in dry ice (I_DI), liquid nitrogen (I_LN2), or RNA later ™ (I_RL) before RNAseq analysis. Alternatively, liver and quadriceps samples were dissected from partially thawed frozen carcasses of mice that were euthanized with pentobarbital/phenytoin (Euthasol ® ) then preserved in dry ice (C_DI), liquid nitrogen (C_LN2), or segmented into thirds and preserved in RNA later™ (C_RL) before RNAseq analysis. A) Principal component analysis of liver samples. Percent variance for each principal component (PC) is shown. B) Uniformity of gene body coverage in liver samples. C) Principal component analysis of quadriceps samples. Percent variance for each principal component (PC) is shown. D) Uniformity of gene body coverage in quadriceps samples. (*** = p < 0.001, ** = p < 0.01, * = p < 0.05, ns = no significance, Mann–Whitney U test).

Article Snippet: Raw RNA sequence data from the RR-1 NASA Validation flight liver (GLDS-48 and GLDS-168) samples, RR-1 CASIS liver samples (GLDS-47), and the ground-based studies designed to simulate and assess spaceflight euthanasia, carcass and tissue preservation, and/or storage protocols, GLDS-49, GLDS-235, and GLDS-236 were analyzed using the GeneLab standard RNAseq analysis pipeline.

Techniques: MANN-WHITNEY

Journal: Acta Neuropathologica Communications

Article Title: Metabolic and transcriptomic profiles of glioblastoma invasion revealed by comparisons between patients and corresponding orthotopic xenografts in mice

doi: 10.1186/s40478-021-01232-4

Figure Lengend Snippet: Baseline information of patients and PDOX

Article Snippet: Preprocessing of RNA sequencing (RNAseq) data was performed following the standard pipeline and recommendations from bcbio-nextgen (version 1.0.4, http://bcbio-nextgen.readthedocs.org/en/latest/ ).

Techniques:

Journal: bioRxiv

Article Title: ATF4 and EcR interact to mediate both transcriptional activation and repression in the Drosophila fat body

doi: 10.64898/2026.03.10.710866

Figure Lengend Snippet: Counts per million (CPM) for the indicated transcripts from the RNAseq analysis in . ****=p<0.00001; ***=p<0.0001; **=p<0.001; *=p<0.05. Only significant comparisons are shown. Statistical tests are described in the methods.

Article Snippet: Duplicate RNA samples from independent crosses were submitted for each genotype to the Plasmidsaurus RNAseq analysis pipeline.

Techniques: RNA sequencing

Journal: bioRxiv

Article Title: ATF4 and EcR interact to mediate both transcriptional activation and repression in the Drosophila fat body

doi: 10.64898/2026.03.10.710866

Figure Lengend Snippet: A) Table summarizing the overall count of differentially regulated genes in RNAseq analyses performed in isolated fat bodies where the indicated RNAi lines are driven by Dcg-GAL4 . B) Venn-diagram showing the commonalities in the differentially downregulated (left) and upregulated genes (right) in A. C-E) Counts per million (CPM) for the indicated transcripts from the RNAseq analysis in A . C and D show data for known EcR targets, E shows data for known ATF4 targets. Also see Table S1 and S2 . ****=p<0.00001; ***=p<0.0001; **=p<0.001; *=p<0.05. Only significant comparisons are shown. Statistical tests are described in the methods.

Article Snippet: Duplicate RNA samples from independent crosses were submitted for each genotype to the Plasmidsaurus RNAseq analysis pipeline.

Techniques: RNA sequencing, Isolation