Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Seq data for five HER2 over-expressed samples with twelve green fluorescent protein control samples using human mammary epithelial cells

ABSTRACT: Purpose: The goal was to capture the transcriptional activity due to over-expression of HER2 protein. We profiled this transcriptional activity using two different RNA-Seq alignment and quantification pipelines. We also used these samples to generate a gene expression signature of HER2 pathway activity. Over-expression was validated using Western blots. Illumina RNA-Seq technology was used to capture the downstream transcriptional activity. Reads were 101 base pairs long and single ended. An R open source package “Rsubread” was used to align and quantify the read using UCSC hg19 annotation. The integer-based gene counts were later normalized in FPKM and TPM .

ORGANISM(S): Homo sapiens

PROVIDER: GSE62820 | GEO | 2015/06/01

SECONDARY ACCESSION(S): PRJNA265215

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA-Seq data for AKT, BAD, ERBB2, IGF1R, RAF1 and KRAS(G12V) overexpressed samples with twelve green fluorescent protein control samples using human mammary epithelial cells

Project description:The goal was to capture the transcriptional activity due to over-expression of AKT, BAD, ERBB2, IGF1R, RAF1 and KRAS(G12V) genes .Overexpressions were validated using Western Blots. Illumina RNA-Seq technology was used to capture the downstream transcriptional activity. Reads were 101 base pairs long and single ended. An R open source package “Rsubread” was used to align and quantify the read using UCSC hg19 annotation. The integer-based gene counts were later normalized in TPM .

2017-06-01 | GSE83083 | GEO

RNA-Seq data for AKT, BAD, ERBB2, IGF1R, RAF1 and ERK1 over-expressed samples with twelve green fluorescent protein control samples using human mammary epithelial cells

Project description:The goal was to capture the transcriptional activity due to over-expression of AKT, BAD, ERBB2, IGF1R, RAF1 and ERK1 genes.Over-expressions were validated using Western Blots. Illumina RNA-Seq technology was used to capture the downstream transcriptional activity. Reads were 101 base pairs long and single ended. An R open source package “Rsubread” was used to align and quantify the read using UCSC hg19 annotation. The integer-based gene counts were later normalized in TPM .

2017-01-01 | GSE73628 | GEO

RNA-Seq data for KRAS wild-type(WT) and two mutant forms G12V and Q61H over-expressed samples with green fluorescent protein control samples using human mammary epithelial cells

Project description:The goal was to capture the transcriptional activity due to over-expression of KRAS gene. Over-expressions were validated using Western Blots. Illumina RNA-Seq technology was used to capture the downstream transcriptional activity. Reads were 101 base pairs long and single ended. An R open source package “Rsubread” was used to align and quantify the read using UCSC hg19 annotation. The integer-based gene counts were later normalized in TPM .

2017-05-01 | GSE76877 | GEO

RNA-Seq data for KRAS wild-type(WT) and two mutant forms G12V and Q61H over-expressed samples with green fluorescent protein control samples using human mammary epithelial cells

Project description:The goal was to capture the transcriptional activity due to over-expression of KRAS gene. Over-expressions were validated using Western Blots. Illumina RNA-Seq technology was used to capture the downstream transcriptional activity. Reads were 101 base pairs long and single ended. An R open source package âRsubreadâ was used to align and quantify the read using UCSC hg19 annotation. The integer-based gene counts were later normalized in TPM . Profiles of gene expression were generated in cells derived from breast and used to generate a gene-expression signatures.

2017-05-01 | E-GEOD-76877 | biostudies-arrayexpress

Alternatively processed and compiled RNA-Sequencing and clinical data for thousands of samples from The Cancer Genome Atlas

Project description:We reprocessed RNA-Seq data for 9264 tumor samples and 741 normal samples across 24 cancer types from The Cancer Genome Atlas with "Rsubread". Rsubread is an open source R package that has shown high concordance with other existing methods of alignment and summarization, but is simple to use and takes significantly less time to process data. Additionally, we provide clinical variables publicly available as of May 20, 2015 for the tumor samples where the TCGA ids are matched.

2015-01-27 | GSE62944 | GEO

Epigenetic analysis of twelve human normal breast tissue samples

Project description:Illumina Human Methylation 450k Beadchip of 12 human normal breast tissue samples

2019-08-06 | GSE124367 | GEO

Kinase activity profiling in breast cancer samples

Project description:In this study, we measured the kinase activity profiles of 32 pre-treatment tumour biopsies of HER2-positive breast cancer patients. The aim of this study was to assess the prognostic potential of kinase activity levels in prediction of treatment success against HER2-targeted therapy combined with chemotherapy. Indeed, our system-wide kinase activity analysis, based on targeted mass spectrometry measurement of kinase activation loops, allowed us to link kinase activity to treatment response. Overall, high kinase activity in the HER2-pathway was associated with good treatment outcome. Furthermore, we found eleven kinases differentially regulated between treatment outcome groups.

2024-03-09 | PXD035186 | panorama

Fluorescent cholangiography: An up-to-date overview twelve years after the first clinical application.

Project description: Not available

| S-EPMC8476339 | biostudies-literature

RNA-seq data from murine eGFP+ relbfl/flnfkb2fl/flCg1-Cre and Cg1-Cre splenic germinal center B cells purified by fluorescent activated cell sorting.

Project description:RNA-seq analysis of murine eGFP+ relbfl/flnfkb2fl/flCg1-Cre and Cg1-Cre splenic germinal center B cells identifies genes regulated by the transcription factors RELB and p52 (NF-kB2) in germinal center B cells. Germinal center B cells from 12-week old relbfl/flnfkb2fl/flCg1-Cre and Cg1-Cre littermate mice immunized with sheep red blood cells (SRBC) were isolated at day 7 after immunization by flow cytometric sorting from splenic mononuclear cells. RNA was isolated, amplified and submitted for RNA-sequencing on an Illumina HiSeq2500 instrument for 35-40 million 2x50 paired-ended reads.

2016-07-01 | E-GEOD-77374 | biostudies-arrayexpress

Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FNA samples)

Project description:The Formalin-Fixed Paraffin-Embedded (FFPE) samples on selected breast cancer subtypes (ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2-) and their paired fresh fine needle aspirated biopsies (FNA) were investigated. The cases represented different subtypes of breast cancers based on their clinical receptors ER (E) and Her2 (H) status to demonstrate the ability of gene profiles to differentiate these tumors. Compared to FNA specimens, FFPE samples yielded relatively more degraded RNA, and 80% of the samples deemed suitable for cDNA-mediated annealing, selection, extension and ligation (DASL) assay. It is able to demonstrate that gene profiles from FFPE microarrays were reproducible and correlated well with the corresponding gene profiles from FNA microarrays. The gene profiles from both FNA and FFPE could differentiate the four breast cancer subtypes, and the expression levels of corresponding gene set were consistent with qRT-PCR and correlated to the clinical outcomes on published microarray data. It supports the use of FFPE specimens to develop a prognostic tool for breast cancers which can obviate the need for fresh specimens. 25 FNA specimens were processed for direct hybridization assays using Illumina Human-Ref8 version 3 BeadChips. Invasive ductal carcinoma (IDC)-type subtypes ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2- (ER: estrogen receptor, HER2: human epidermal growth factor receptor 2) were analyzed.

2011-06-22 | E-GEOD-23385 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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