Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigating the altered brain metastatic transcriptome in breast cancer

ABSTRACT: Brain metastatic disease occurs in 10-30% of metastatic breast cancer cases. The incidence of brain metastases is increasing with median overall survival < 2 years for patients. In order to better characterize oncogenic pathway activity pertinent to breast cancer brain metastasis, exome capture RNA sequencing was carried out on patient matched primary breast with brain metastatic tumor samples for 45 cases of breast cancer brain metastasis (N= 90 samples). Here, exome capture RNA sequencing data is deposited as sequencing batch corrected log2 transformed trimmed M of means (TMM) normalized counts per million (CPM) (log2(TMM-CPM +1) gene expression values (n=16,714 protein coding genes; N=90 tumor samples).

ORGANISM(S): Homo sapiens

PROVIDER: GSE184869 | GEO | 2021/11/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Investigating the altered brain metastatic transcriptome in breast cancer

Project description:Brain metastatic disease occurs in 10-30% of metastatic breast cancer cases. The incidence of brain metastases is increasing with median overall survival < 2 years for patients. In order to better characterize oncogenic pathway activity pertinent to breast cancer brain metastasis, exome capture RNA sequencing was carried out on patient matched primary breast with brain metastatic tumor samples for 45 cases of breast cancer brain metastasis (N= 90 samples). Here, exome capture RNA sequencing data is deposited as sequencing batch corrected log2 transformed trimmed M of means (TMM) normalized counts per million (CPM) (log2(TMM-CPM +1) gene expression values (n=16,714 protein coding genes; N=90 tumor samples).

2022-04-01 | GSE173661 | GEO

RET overexpression leads to increased brain metastatic competency in luminal breast cancer patients

Project description:Breast cancer brain metastasis is a rising occurrence, necessitating a better understanding of the mechanisms involved for effective management. Breast cancer brain metastases diverge significantly from the primary tumor, with gains in kinase and concomitant losses of steroid signaling observed. In this study, we explored the role of the kinase receptor RET in promoting breast cancer brain metastasis and provide a rationale for targeting the receptor in this patient cohort. Here, exome capture RNA sequencing data is deposited as sequencing batch corrected log2 transformed trimmed M of means (TMM) normalised counts per million (CPM) (log2(TMM-CPM +1) gene expression values for the patients described in this study (n=19,622 protein coding genes; N=16 tumour samples).

2024-06-25 | GSE268217 | GEO

Quantitative Proteomics by SWATH-MS reveals molecular differences among malignant and benign breast tumors in Mexican woman

Project description:Breast tumors are produced by an uncontrollable cell proliferation mechanism and can be classified as benign (TMB) or malignant (TMM). TMM or breast cancer is the neoplasia with the highest incidence and mortality in Mexican women. Over time, some types of TMB can transform into a TMM. However, the mechanisms involved in such processes remain elusive and limited studies have examined the molecular differences between TMB and TMM. Hence, the aim of this study was to evaluate and compare the proteomic profile of TMB (n = 10) and TMM (n = 6) of Mexican women.

2024-10-22 | PXD019334 | Pride

APA usage in vaporized cannabis plant matter (CPM) exposure rats

Project description:Role of alternative polyadenylation (APA) in rat brain after vaporized cannabis plant matter (CPM) exposure remains largely undetermined. Our WTTS-seq approach to capture 3'-end of RNAs clearly revealed alternative polyadenylation events responsible for dominantly down-regulates APA expression on Glutamatergic Transcripts in rats after CPM Exposure.

2019-06-05 | GSE115534 | GEO

RNA-sequencing for dynamic epi-transcriptomic landscape mapping with disease progression in patient primary breast tumours.

Project description:Advanced breast cancer is characterised by enhanced tumour adaptability to therapeutic pressure and the metastatic microenvironment. Transcriptome differences in 14 primary breast tumour samples (n = 14 samples) are uncovered through this comparative RNA-seq analysis of patients that responded well to therapy (n = 7) and patients who had disease recurrence on endocrine treatment (n = 7). RNA sequencing data is deposited as log2 transformed median-of-ratios (DESeq2) normalised counts gene expression values (44934 genes IDs; n = 14 tumour samples).

2023-05-16 | GSE214789 | GEO

Gene expression analysis of Lgr5/Tspan8 expressing cells in the adult mammary gland

Project description:Purpose: The aim of this study is to identify genes that are differentially expressed in the different basal cell populations defined by Lgr5 and Tspan8 (T8) expression from adult mouse mammary glands. Methods: Total RNA was extracted from sorted basal populations defined by Lgr5 and Tspan8 expression from the mammary glands of 10-week-old Lgr5-GFP-IRES-creERT2 female mice. Total RNA (50 ng) for each of the two biological replicates was used to generate libraries for whole-transcriptome analysis following Illumina's TruSeq RNA v2 sample preparation protocol. Libraries were sequenced on an Illumina HiSeq 2000 at the Australian Genome Research Facility (AGRF), Melbourne. At least 20 million 100 bp single-end reads were obtained for each sample. Reads were aligned to the mouse genome mm10 using Rsubread version 1.8.0. The number of reads overlapping each Entrez gene was counted using RefSeq gene annotation and featureCounts. Filtering and normalization used the edgeR package. Genes were filtered as unexpressed if their count per million (CPM) was less than 0.5 in fewer than 2 samples. Compositional differences between libraries were normalized using the trimmed mean of M-values (TMM) method. Differential expression was analyzed using the limma package. Counts were transformed to log2-CPM values with associated precision weights using voom. Differential expression was assessed using moderated t-statistics. Genes were considered to be differentially expressed if they achieved a false discovery rate of 5% and a fold-change in excess of 2.

2017-01-31 | GSE73111 | GEO

Differentiation of IMR32 neuroblastoma is accompanied by a global change in the transcriptome

Project description:The aim of this study is to compare human transcriptomes based on NGS (RNA-seq). The transcriptome of neuroblastoma IMR32 was compared with the transcriptome of neuroblastoma IMR32, which was differentiated for 16 days in the presence of 2.5 mkM BrdU. Methods. Human mRNA profiles of 16-day differentiation of IMR32 neuroblastoma and non-differentiated IMR32 neuroblastoma were obtained by deep three-fold sequencing using Illumina NovaSeq. The mapping is read into the human genome (hg38) using the hisat program. On average, about 89-90% of all data received was unambiguously aligned in each library. The htseq-count utility has counted the number of reads that have been matched against known genes (ncbi - entrezID). The obtained values (cpm - countpermillion) for each gene for each library were combined into one matrix for further analysis. Results: Using an optimized data analysis workflow, we matched about 30 million sequence reads per sample to the human genome (hg38). Filtration, normalization by the method (TMM), variance estimation and differentially expressed genes estimation were performed in the edgeR module. Genes in which the cpm did not exceed 1 in any three libraries were considered low expressing.

2020-12-18 | GSE161759 | GEO

Comparison of poly(A) and capture RNA-seq: controlled degradation in vitro

Project description:We compare the performance of two library preparation protocols (poly(A) and exome capture) in in vitro degraded RNA samples

2015-08-03 | GSE64113 | GEO

Whole exome sequencing of NT2.5 and NT2.5-LM cell lines

Project description:NT2.5-LM is a cell line derived from the parental NT2.5 cell line that provides a more proliferative and metastatic murine model of breast cancer. We used whole exome sequencing to examine mutational differences.

2024-06-30 | GSE261253 | GEO

Metastatic breast cancer to the brain: implications of the local microenvironment for colonization and treatment

Project description:This SuperSeries is composed of the following subset Series: GSE14682: Metastatic breast cancer to the brain: set 1 GSE14683: Metastatic breast cancer to the brain: set 2 Refer to individual Series

2010-06-24 | E-GEOD-14690 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data