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Sorted BCC timecourse after Vismo treatment - MCT, 6d, 14d

ABSTRACT: K14Cre-ER; Ptch1fl/fl; p53fl/fl;Lgr5GFP mice were aged until the appropriate tumor density was achieved. Skin samples were taken from control mice (untreated) or mice treated for 6 days or 14 days at twice a day dosing with vismodegib (75mg/kg body weight). RNA was extracted from freshly FACS sorted tumor cells based on GFP intensity. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0014328

ORGANISM(S): Mus musculus

PROVIDER: GSE116961 | GEO | 2018/08/08

REPOSITORIES: GEO

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ATAC sequencing of sorted BCC cells after vismodegib treatment

Project description:K14Cre-ER; Ptch1fl/fl; p53fl/fl;Lgr5GFP mice were aged until the appropriate tumor density was achieved. Skin samples were taken from control mice (untreated) or mice treated for 6 days or 14 days at twice a day dosing with vismodegib (75mg/kg body weight). RNA was extracted from freshly FACS sorted tumor cells based on GFP intensity. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.

2018-08-08 | GSE116965 | GEO

Profiling of untreated and residual murine BCC after Hedgehog Pathway Inhibitor

Project description:RNA was isolated from laser capture micro-dissected (LCM) tumour nests from fresh frozen skin of K14Cre-ER; Ptch1fl/fl; p53fl/fl mice either before (untreated) or after (treated) 28 days of twice a day vismodegib dosing at 75mg/kg body weight by oral gavage. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0014355

2018-08-08 | GSE101504 | GEO

Sorted BCC timecourse after Vismo treatment - MCT, 6d, 14d

Project description:Sorted BCC timecourse after Vismo treatment - MCT, 6d, 14d

| PRJNA480703 | ENA

Single-cell RNA-seq of embryonic day 17 (E17) mouse skin epithelial cells with or without Mettl3 knockout

Project description:We employed single-cell RNA sequencing to examine effects on steady-state RNA levels induced by METTL3 depletion in mouse skin epithelium during morphogenesis. YFP+ epidermal cells were isolated from E17 embryos with Mettl3 fl/+, Rosa16-YFP fl/+, K14Cre (Ctrl) and Mettl3 fl/fl, Rosa16-YFP fl/+, K14Cre (cKO) genotypes through FACS. Trypan blue staining indicates the ratio of living cells in each sample is >90%. 8000 single cells from each sample is processed with the Chromium™ Single Cell 3’ Library and Gel Bead Kit (V2) (10× Genomics, 120267) to prepare single-cell RNA-seq libraries, which is sequenced on Illumina NextSeq 500 sequenceras 26 × 57 × 8.

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Undifferentiated Pleomorphic Sarcoma Model Using Tumors from BrafCa

Project description:Analysis of undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma like tumors from BrafCa, p53Fl/Fl mouse model of soft tissue sarcoma

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Undifferentiated Pleomorphic Sarcoma Model

Project description:Analysis of undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma-like tumors from LSL-KrasG12D, p53Fl/Fl mouse model of soft tissue sarcoma.

2009-11-21 | GSE16779 | GEO

RNA Sequencing Quantitative Analysis of cell lines derived from tumours from two mouse models of human osteosarcoma that recapitulate clinically distinct human osteosarcoma subtypes.

Project description:Purpose: Osteosarcoma (OS) is the most common primary bone malignancy. OS consists of several subtypes including fibroblastic, osteoblastic and chondroblastic OS. We have developed genetically engineered mouse models of human OS that recapitulate two distinct subtypes, fibroblastic (Osx-CreLox p53-/- Rb-/-) and osteoblastic (Osx-Cre shRNA p53-/-) OS. The goal of this study was to identify transcriptional differences that distinguish the two subtypes. Methods: mRNA profiles of cell lines derived from tumours from Osx-Cre p53fl/fl Rbfl/fl (fibroblastic OS) and Osx-Cre shRNA TRE-p53.1224 pRbfl/fl (osteoblastic OS) mouse models were generated by RNA sequencing, in triplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 12,436 transcripts in the tumours of Osx-Cre p53fl/fl Rbfl/fl and 12,074 Osx-Cre shRNA TRE-p53.1224 pRbfl/fl with the TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes. Conclusions: Our study represents a detailed analysis of OS subtype transcriptomes generated by RNA-seq technology. mRNA profiles of cell lines derived from tumours from two genetically engineered mouse models of human osteosarcoma (Osx-Cre p53fl/fl Rbfl/fl and Osx-Cre shRNA TRE-p53.1224 pRbfl/fl) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

2015-07-06 | E-GEOD-58916 | biostudies-arrayexpress

Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma

Project description:Purpose: We have used microarrays to identify gene expression profiles that distinguish mouse OS cells from normal pre-osteoblast cells and mature osteoblast cells. Methods: Transcriptional profiles of three cell lines derived from tumors from Osx-Cre p53fl/fl Rbfl/fl (fibroblastic OS) mouse model, and from pre-osteoblast cells (Kusa4b10 mouse bone marrow stromal cell line) and osteoblast cells (derived by in vitro differentiation of the Kusab410 mouse bone marrow stromal cell line) were generated by microarray analysis, each in triplicate, using Affymetrix mouse Gene1.0ST arrays. Transcriptional profiles were analyzed in cell lines derived from tumors from a genetically engineered mouse model of human osteosarcoma (Osx-Cre p53fl/fl Rbfl/fl) and osteoblast cells derived from the Kusa4b10 mouse bone marrow stromal cell line, in the undifferentiated state (pre-osteoblasts) and differentiated state (osteoblasts).

2015-01-29 | E-GEOD-63939 | biostudies-arrayexpress

Chromosomal deletions linked to p53 loss of heterozygosity promote cancer through p53-independent mechanisms

Project description:The purpose of current study is to identify the differentiated gene expression associated with mouse 11B3 deletion, syntenic to human chromosome 17p13.1. We compared four different mouse acute myeloid leukemia cells, freshly isolated from mouse bone marrows with either 11B3fl/p53fl;shNf1;shMll3;Vav1-Cre or p53fl/fl;shNf1;shMll3;Vav1-Cre. The RNA-seq results indicate that genes located on chromosome 11B3 mostly reduce gene expression level in 11B3 deleted leukemia cells.

2016-04-04 | GSE69654 | GEO

Role of polycomb repressive complex 1 in the intestinal homeostasis [RNA-Seq]

Project description:These data include RNA Seq data generated from wild type and Ring1a Ring1b dKO ISCs from Lgr5Gfp-CreERT2, Lgr5Gfp-CreERT2 Ring1a-/- Ring1bf/f, Lgr5Gfp-CreERT2-Ctnnb1-ex3 and Lgr5Gfp-CreERT2 Ring1a-/- Ring1bf/f-Ctnnb1-ex3 mice. Total RNA extracted from sorted wild type and Ring1a Ring1b dKO ISCs.

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