Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microenvironment Cell Populations Affymetrix HuGene 1.0ST

ABSTRACT: Human tissues harbour a wide array of cellular populations, often including both immune and lymphoid cell populations, endothelial cells and fibroblasts. The goal of this study was to identify transcriptomic markers of these cell populations, in order to quantify their abundances using transcriptomic data. The present super-series is composed of a large number of transcriptomic profiles of these cell populations. These profiles were obtained from public repositories, normalized using the fRMA R package (which allows a consistent normalization of profiles across public series), and consistently annotated. This series corresponds to Affymetrix HuGene 1.0ST profiles. Sample's annotation is available as supplementary material.

ORGANISM(S): Homo sapiens

PROVIDER: GSE86357 | GEO | 2016/09/02

SECONDARY ACCESSION(S): PRJNA341516

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Microenvironment Cell Populations Affymetrix 133 A

Project description:Human tissues harbour a wide array of cellular populations, often including both immune and lymphoid cell populations, endothelial cells and fibroblasts. The goal of this study was to identify transcriptomic markers of these cell populations, in order to quantify their abundances using transcriptomic data. The present super-series is composed of a large number of transcriptomic profiles of these cell populations. These profiles were obtained from public repositories, normalized using the fRMA R package (which allows a consistent normalization of profiles across public series), and consistently annotated. This series corresponds to Affymetrix 133 A profiles. Sample's annotation is available as supplementary material.

2016-09-02 | GSE86363 | GEO

Microenvironment Cell Populations Affymetrix 133 Plus 2.0 series

Project description:Human tissues harbour a wide array of cellular populations, often including both immune and lymphoid cell populations, endothelial cells and fibroblasts. The goal of this study was to identify transcriptomic markers of these cell populations, in order to quantify their abundances using transcriptomic data. The present super-series is composed of a large number of transcriptomic profiles of these cell populations. These profiles were obtained from public repositories, normalized using the fRMA R package (which allows a consistent normalization of profiles across public series), and consistently annotated. This series corresponds to Affymetrix 133 Plus 2.0 profiles. Sample's annotation is available as supplementary material.

2016-09-02 | GSE86362 | GEO

Homo sapiens

Project description:Microenvironment Cell Populations Affymetrix HuGene 1.0ST

| PRJNA341516 | ENA

A Novel RNA Sequencing Data Analysis Method for Cell Line Authentication

Project description:We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. Using both public and novel data, we demonstrate the use of RNA-sequencing data analysis for cell line authentication by examining the validity of COLO205, DLD1, HCT15, HCT116, HKE3, HT29 and RKO colorectal cancer cell lines. We successfully authenticate the studied cell lines and validate previous reports indicating that DLD1 and HCT15 are synonymous. We also show that the analysed HKE3 cells harbour an unexpected KRAS-G13D mutation and confirm that this cell line is a genuine KRAS dosage mutant, rather than a true isogenic derivative of HCT116 expressing only the wild type KRAS. This authentication method could be used to revisit the numerous cell line based RNA sequencing experiments available in public data repositories, analyse new experiments where whole genome sequencing is not available, as well as facilitate comparisons of data from different experiments, platforms and laboratories.

2017-02-14 | GSE81194 | GEO

Expression data of myeloma CD138+ and CD138- populations

2013-07-17 | GSE31305 | GEO

Gene expression data from non-infected and M. hyorhinis-infected gastric cancer cell lines using Affymetrix genechip (HuGene-1_0-st)

Project description:Chronic infection of M. hyorhinis is postulated to be associated with cancer cell migration and invasion. To explore the mechanisms of M. hyorhinis-promoted invasiveness, we performed Affymetrix genechip (HuGene-1_0-st) analysis to examine differential gene expression profiles between non-infected and infected gastric cancer cells. We used microarrays to detail global programme of gene expression and identified distinct classes of upregulated genes after M. hyorhinis infection of gastric cancer cell lines.

2013-11-22 | GSE52638 | GEO

Transcriptional profiling of striatum from 6-month-old mice heterozygous knockout for 52 genes and corresponding wildtype control mice

Project description:As part of collaboration between the X. William Yang Lab at UCLA and CHDI, a list of 52 genes that were implicated in Huntington’s disease (HD) through various computational modeling efforts was compiled, and murine lines with heterozygous knockout of these genes were obtained from public repositories or newly created. Striatum was dissected from 6-month-old mice that were either heterozygous KO for one of 52 genes or the corresponding wildtype (WT) controls. Transcriptomic analysis (RNASeq) was performed.

2022-10-19 | GSE149900 | GEO

Gene expression data from non-infected and M. hyorhinis-infected gastric cancer cell lines using Affymetrix genechip (HuGene-1_0-st)

2013-11-22 | E-GEOD-52638 | biostudies-arrayexpress

Expression data of myeloma CD138+ and CD138- populations

Project description:Comparison of gene expression profiles between CD138+ and CD138- populations from human myeloma cell lines RPMI-8226 and NCI-H929. We used Affymetrix human gene 1.0ST array and analyzed with GeneSpring GX. CD138+ and CD138- subsets of cells were separated using FACS and clonogenecity of both population were compared. The RNA was extracted and hybridized with Affymetrix Human Gene 1.0ST array.

2013-07-17 | E-GEOD-31305 | biostudies-arrayexpress

Systematic reanalysis of co-fractionation mass spectrometry data

Project description:A total of 206 co-fractionation mass spectrometry (CF-MS) experiments were downloaded from public proteomics repositories such as PRIDE and MASSIVE, then re-analyzed with MaxQuant.

2021-04-20 | PXD022048 | Pride

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