Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequencing of Coding and Non-coding Regions in Primary Breast Cancers and Patient-Matched Controls

ABSTRACT: Sequencing of Coding and Non-coding Regions in Primary Breast Cancers and Patient-Matched Controls

PROVIDER: PRJNA353973 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Sequencing of Coding and Non-coding Regions in Primary Breast Cancers and Patient-matched Controls

Project description:<p>Genomic analysis of tumor samples has led to the identification of hundreds of cancer genes based on the presence of mutations in protein-coding regions. By contrast, much less is known about cancer-causing mutations in non-coding regions. Here, we performed deep sequencing in 360 primary breast cancers and developed computational methods to identify significantly mutated promoters. Clear signals were found in the promoters of four genes. FOXA1, a known driver of hormone-receptor positive breast cancer, harbors a mutational hotspot in its promoter that leads to overexpression through increased E2F binding. RMRP and NEAT1, two non-coding RNA genes, carry mutations that alter protein binding to the promoter and impact expression levels. Overall, our study shows that recurrent mutations in or near gene promoters in cancers have functional consequences. Power analyses indicate that more such genes remain to be discovered through deep sequencing of adequately sized patient cohorts. </p>

| phs001250 | dbGaP

Homo sapiens

Project description:Sequencing of Coding and Non-coding Regions in Primary Breast Cancers and Patient-Matched Controls

| PRJNA353974 | ENA

Differential Mutations In Matched Primary and Metastatic Colorectal Cancers

Project description:Differential Mutations In Matched Primary and Metastatic Colorectal Cancers

| PRJNA314364 | ENA

Genomic Profile of Primary Colorectal Cancers and associated Liver Metastases

Project description:Comparison of genomic alterations of primary colorectal cancers with liver metastases of the same patient Keywords: array CGH, colorectal cancer, colon cancer, liver metastasis 21 primary colorectal cancers and 21 matched liver metastases hybridized against sex-matched control pools

2010-07-07 | E-GEOD-10179 | biostudies-arrayexpress

Gene expression in human oral mucosal fibroblasts and patient-matched skin fibroblasts

Project description:Wound healing within the oral mucosa results in minimal scar formation compared to wounds within the skin. We have recently demonstrated distinct differences in the ageing profiles of cells (oral mucosal and patient-matched skin fibroblasts) isolated from these tissues. We hypothesize that the increased replicative potential of oral mucosal fibroblasts may confer upon them preferential wound healing capacities. Passage-matched early cultures of oral mucosal fibroblasts and skin fibroblasts demonstrated distinct gene expression profiles with a number of genes linked to wound healing/tissue repair. We analyzed the gene expression profiles of oral mucosal and patient-matched skin fibroblasts for multiple patients both prior to (0h) and (6h) following a wounding stimulus.

2011-01-01 | GSE21648 | GEO

Gene expression changes in patient-matched gastric normal mucosa, adenomas, and carcinomas

Project description:sequential changes in gene expression profiles in the gastric adenoma-carcinoma sequence by analyzing eight patient-matched gastric normal mucosa, adenomas and carcinomas.

2010-09-28 | GSE24375 | GEO

Transcriptomic profiling of a glioblastoma multiforme patient with matched control brain tissue

Project description:To investigate differential gene expression, we analyzed the entire transcriptomes of tumor and matched normal brain tissues obtained from a patient who had glioblastoma multiforme. We extracted and sequenced the mRNA using Illumina GA2 platform. The raw data was analyzed using our recently developed program called RNASEQR, as well as ERANGE, MapSplice, SpliceMap, and TopHat. Tumor and matched control brain tissues were obtained from a Han-Chinese patient.

2011-10-30 | E-GEOD-33328 | biostudies-arrayexpress

A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome [WGS]

Project description:Many cancers are organized as cellular hierarchies sustained by cancer stem cells (CSC), whose eradication is crucial for achieving long-term remission. Difficulties to isolate and undertake in vitro and in vivo experimental studies of rare CSC under conditions that preserve their original properties currently constitute a bottleneck for identifying molecular mechanisms involving coding and non-coding genomic regions that govern stemness. We focussed on acute myeloid leukemia (AML) as a paradigm of the CSC model and developed a patient-derived system termed OCI-AML22 that recapitulates the cellular hierarchy driven by leukemia stem cells (LSC). Through classical flow sorting and functional analyses, we established that a single phenotypic population is highly enriched for LSC. The LSC fraction can be easily isolated and serially expanded in culture or in xenografts while faithfully recapitulating functional, transcriptional and epigenetic features of primary LSCs. A novel non-coding regulatory element was identified with a new computational approach using functionally validated primary AML LSC fractions and its role in LSC stemness validated through efficient CRISPR editing using methods optimized for OCI-AML22 LSC. Collectively, OCI-AML22 constitutes a valuable resource to uncover mechanisms governing CSC driven malignancies.

2022-08-23 | GSE211499 | GEO

A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome [ATAC-Seq]

2022-08-23 | GSE211498 | GEO

A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome [RNA-Seq]

2022-08-23 | GSE211595 | GEO