Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole exome and transcriptome sequencing of murine tumor models

ABSTRACT: Whole exome and transcriptome sequencing of murine tumor models

PROVIDER: PRJNA562878 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10043200_1.fastq.gz	Fastqsanger.gz
	SRR10043200_2.fastq.gz	Fastqsanger.gz
	SRR10043201_1.fastq.gz	Fastqsanger.gz
	SRR10043201_2.fastq.gz	Fastqsanger.gz
	SRR10043202_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 170

Similar Datasets

Whole exome and transcriptome sequencing of murine tumor models

Project description:These data were used for prediction of neoantigens and minor histocompatibility mismatch antigens, which were subsequently used for design of a machine-learning algorithm for tumor-specific antigen (TSA) immunogenicity prediction. TSA vaccines are a growing area of study for cancer immunotherapy, but identification of clinically relevant targets remains a challenge. The study associated with these data provides the first description of a computational method for direct prediction of TSA immunogenicity trained entirely from validated TSA immunogenicity scores. This tool has allowed us to 1) predict for clinically efficacious TSA targets, 2) identify genomic correlates of TSA immunogenicity, and 3) demonstrate evidence of alternative out-of-frame TSAs which can promote anti-tumor immunity.

2019-09-03 | GSE136619 | GEO

Exome sequencing analysis of murine medulloblastoma models identifies Wdr11 as a potential tumor suppressor in Group 3 tumors

Project description:We previoiusly identified WDR11 as a potential tumor suppressor in murine medulloblastoma models. To determine additional genes/pathways affected by WDR11 overexpression.To compare somatic mutations of murine models with human medulloblastoma (MB), we performed whole-exome sequencing of mouse tumors representing three distinct MB subgroups: Wnt, Sonic Hedgehog (Shh) and Group 3 (G3). 64 somatic mutations were identified and validated, including 40 predicted to cause amino acid changes. After filtering and cross-species analysis with 366 human MBs from four independent studies, human orthologs for 16 of the 40 mouse genes were found to harbor non-silent mutations in human MB. Loss-of-function Mll2 mutations detected in one mouse tumor were previously reported in 30 of 366 human MBs. In mice with G3 MB, one mouse that died at least 15 days earlier than the others had four novel candidate genes harboring non-silent somatic mutations, Lrfn2, Smyd1, Ubn2 and Wdr11. To test whether these genes had tumor suppressive activity, we constitutively overexpressed each wild type gene in murine G3 tumorspheres followed by intracranial implantation. Mice harboring mouse G3 MB overexpressing WDR11 showed extended survival compared to the other three genes. Genes in the KEGG WNT signaling pathway, including Ccnd1/2/3, Myc and Tcf7l1, were down-regulated in G3 MB tumorspheres overexpressing WDR11, consistent with reduced tumor progression. In conclusion, we demonstrated that common spontaneous mutations were shared between human and murine models of MB suggesting similar molecular mechanisms of tumorigenesis, and identified WDR11 as a protein with tumor suppressive activity in G3 MB.

2017-10-17 | GSE101767 | GEO

MM in murine models: WES

Project description:Characterization of the mutational landscape of the 5T murine models for multiple myeloma, by whole-exome sequencing.

2018-10-09 | E-MTAB-5282 | biostudies-arrayexpress

Gene expression profiling of MYC inducible murine tumor models

Project description:Gene expression profiling of MYC inducible murine tumor models

| PRJNA599413 | ENA

ID8 whole exome sequence

Project description:The data in this submission relate to whole exome sequencing from murine ovarian cancer cell line ID8. All sequencing was performed by Beckman Coulter Genomics, Grenoble, France in February 2013.

2018-03-31 | E-MTAB-4663 | biostudies-arrayexpress

Characterisation of murine syngeneic tumor models

Project description:Characterisation of murine syngeneic tumor models enables rational preclinical model selection for immuno-oncology drug discovery

| PRJEB12925 | ENA

Cervical Adenocarcinoma Whole Exome sequencing

Project description:Raw data of exome sequencing of 17 paired samples and 1 orphan tumor sample, total 18 samples

2022-02-12 | E-MTAB-9766 | biostudies-arrayexpress

Gene expression profiling of MYC inducible murine tumor models (tissues) [microarray]

Project description:Gene expression profiling of MYC inducible murine tumor models (tissues) [microarray]

| PRJNA599414 | ENA

MM in murine models: WES

Project description:MM in murine models: WES

| PRJEB18119 | ENA

Gene expression profiling of MYC inducible murine tumor models (cell lines) [microarray]

Project description:Gene expression profiling of MYC inducible murine tumor models (cell lines) [microarray]