Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression array analysis of tumor-propagating cell populations in human osteosarcoma

ABSTRACT: Gene expression profiling of side population cells (SP) and CD146+ cells from primary human osteosarcoma. We aimed to identify genes that differentially regulated between the tumor propagating cells and the bulk tumor cells. Total RNA was isolated from SP, Non-SP(NSP), CD146+ and CD146- cells. The RNA is converted to cDNA using Nugen Ovation Kit (Nugen, CA, USA) and subjected to Illumina HT-12 array.

ORGANISM(S): Homo sapiens

SUBMITTER: Yuning Tang

PROVIDER: E-GEOD-63390 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression array analysis of tumor-propagating cell populations in human osteosarcoma

Project description:Gene expression profiling of side population cells (SP) and CD146+ cells from primary human osteosarcoma. We aimed to identify genes that differentially regulated between the tumor propagating cells and the bulk tumor cells.

2016-09-01 | GSE63390 | GEO

Gene expression profile of Cxcl12-DsRed+ stromal cells from E15.5, P5, and P10 livers.

Project description:The study is designed to identify transcriptional differences of CD45-Ter119-Cxcl12-DsRed+ stromal cells at different develomental stages. 50,000 CD45-Ter119-Cxcl12-DsRed+ stromal cells from freshly prepared livers of E15.5, P5 and P10 Cxcl12DsRed/+ mice were sorted into Trizol by flow cytometry. Total RNA was isolated and amplified with the WT-Ovation Pico RNA Amplification system (Nugen) as the manufacturer’s instructions. Sense strand complementary DNA was generated using the WT-Ovation Exon Module (Nugen). Then, cDNA was fragmented and labelled using FL-Ovation DNA Biotin Module V2 (Nugen). The labelled cDNA was hybridized to Affymetrix Mouse Gene ST 1.0 chips following the manufacturer's instructions.

2020-10-26 | GSE159308 | GEO

RNA-seq of Maternal Kdm1a mutant 2C embryos and eggs

Project description:2C embryos were generated from Kdm1a FL/Fl Zp3Cre females mated to wild type males for RNA-seq analysis using the Nugen Ovation RNA-seq system V2. Ovulated eggs from Kdm1a FL/Fl Zp3Cre females were isolated for RNA-seq analysis using the Nugen Ovation RNA-seq system V2.

2015-03-10 | GSE66547 | GEO

Comparison between NuGEN's WT-Ovation Pico and One-Direct Amplification Systems

Project description:Differential gene expression between groups of homogenous cell types is a biological question whose time has come. RNA can be extracted from small numbers of cells, such as those isolated by laser capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq. Recently, advances in amplification procedures make amplification directly from whole cell lysates possible. The aim of this study was to compare two amplification systems for variations in observed RNA abundance attributable to the amplification procedure for use with small quantities of cells isolated by laser capture microdissection. Arabidopsis root cells undergoing giant cell formation due to nematode infestation and un-infested control root cells were laser captured and used to evaluate 2 amplification systems. One, NuGEN's WT-Ovation Pico amplification system, uses total RNA as starting material while the other, NuGEN's WT-One-Direct Amplification system, uses lysate containing the captured cells. The reproducibility of whole genome transcript profiling and correlations of both systems were investigated after microarray analysis. The NuGEN WT-Ovation One-Direct system was less reproducible and more variable than the NuGEN WT-Ovation Pico system. The NuGEN WT-Ovation Pico Amplification kit resulted in the detection of thousands of genes differentially expressed genes between giant cells and control cells. This is in marked contrast to the relatively few genes detected after amplification with the NuGEN WT-Ovation One-Direct Amplification kit.

2010-05-26 | GSE21981 | GEO

A novel method of amplification of FFPET derived-RNA enables accurate disease classification with microarrays

Project description:A new method for amplification and labeling of RNA is assessed that permits gene expression microarray analysis of formalin-fixed paraffin embedded tissue (i.e. FFPET) samples. Valid biological data was obtained using gene expression microarrays of diffuse large B-cell lymphoma (i.e. DLBCL) FFPET samples. We examined 59 matched DLBCL patient samples, FFPET and fresh/frozen. The samples contained both prognostic subgroups of DLBCL: germinal center B-cell (i.e. GCB) and activated B-cell (ABC). Fresh/frozen (i.e. FF) samples were amplified by both the traditional Eberwine oligo-dT method and a new method described herein. The matching FFPET samples were also amplified using the new method. This study is a collaboration among Roche Molecular Diagnostics, British Columbia Cancer Agency, National Cancer Institute and Nugen Technologies (the maker of the WT-Ovation FFPET reagents).

2010-06-09 | E-GEOD-19246 | biostudies-arrayexpress

Single cell RNA sequencing data of Side Population and Non-Side Population tumor cells from a mouse model of undifferentiated pleomorphic sarcoma

Project description:We report the application of single-cell RNA sequencing data on Side Population (SP) cells and their Non-Side Population (NSP) counterparts in a mouse model of undifferentiated pleomorphic sarcoma (UPS). SP cells exhibit tumor propagting cell properties characterized by enhanced tumorigenicity and self-renewal potential. The purpose of this experiment is to investigate cellular heterogeneity at the gene expression level in UPS tumors and lineage relationships between different subpopulation of tumor cells. We generated the gene expression profiles of individual cells in the SP and NSP compartments of mouse UPS.

2022-01-07 | GSE162847 | GEO

Epigenetic Based Enrichment of Cancer Stem Cells: Mechanistic and Clinical Implications for Liver Cancer

Project description:Global transcriptiome changes between SP and NSP cells of liver cancer cell lines w and w/o Zebularine treatment

2011-10-04 | GSE24520 | GEO

Nodular lymphocyte predominant hodgkin lymphoma and T cell/histiocyte rich large B cell lymphoma - endpoints of a spectrum of one disease?

Project description:Tumor cells were microdissected from frozen sections of NLPHL and THRLBCL. RNA was amplified using the NUGEN WT-Ovation-One-direct-Kit. Samples were compared to tonsilar germinal center CD77 B cells.

2013-12-01 | GSE47044 | GEO

Identification of ATF2 target genes

Project description:In order to identify transcriptional targets of ATF2, we used a recombinant adenovirus to express constitutively active ATF2 in murine hepatoblasts. Expression of GFP was the control condition. Total RNA was harvested from cells 8 hours post infection. Reverse transcription was performed using Ovation Pico WTA kit (NuGen, 3300-12). Labelling, Encore Biotin Module (NuGen, 4200-12)

2013-11-10 | GSE50530 | GEO

Epigenetic Based Enrichment of Cancer Stem Cells: Mechanistic and Clinical Implications for Liver Cancer

Project description:Global transcriptiome changes between SP and NSP cells of liver cancer cell lines w and w/o Zebularine treatment Huh7,WRL68, KMCH FACS sorted in SP and NSP w and w/o Zebularine and subjected to illumina microarray analysis.

2011-10-03 | E-GEOD-24520 | 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