Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

9afbc3cb-89b6-4944-9c03-2f641af472f8 - samples

ABSTRACT: This dataset contains 86 osteosarcoma samples and their matched normals that underwent RNA sequencing using size fractionation, NuGEN Ovation Ultralow Library System V2 preparation, and paired-end sequencing on Illumina HiSeq 2000.

PROVIDER: EGAD00001008435 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

25d83346-7582-4983-950c-45180aef1f8d - samples

Project description:This dataset contains 86 osteosarcoma samples and their matched normals that underwent RNA sequencing using size fractionation, NuGEN Ovation Ultralow Library System V2 preparation, and paired-end sequencing on Illumina HiSeq 2000.

| EGAD00001008436 | EGA

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

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

Bulk RNA-seq analysis of Type 5 retinal bipolar cells from the Htr3a-GFP line

Project description:15,000 GFP+ cells were collected from two replicates of the Htr3a GFP line into RNAlater (ThermoFisher, AM7024). RNA was purified and bulk RNA-seq was performed using the Ovation RNA-seq system V2 (Nugen, 7102-32)

2016-08-25 | GSE81902 | GEO

Systematic evaluation of RNA-Seq preparation protocol performance (RNASeq: SMARTer)

Project description:In this study, we present a comprehensive evaluation of four RNA-Seq library preparation methods. We used three standard input protocols, the Illumina TruSeq Stranded Total RNA and TruSeq Stranded mRNA kits, and a modified NuGEN Ovation v2 kit; and an ultra-low-input RNA protocol, the TaKaRa SMARTer Ultra Low RNA Kit v3. Our evaluation of these kits included quality control measures such as overall reproducibility, 5’ and 3’ end-bias, and the identification of DEGs, lncRNAs, and alternatively spliced transcripts. Overall, we found that the two Illumina kits were most similar in terms of recovering DEGs, and the Illumina, modified NuGEN, and TaKaRa kits allowed identification of a similar set of DEGs. However, we also discovered that the Illumina, NuGEN and TaKaRa kits each enriched for different sets of genes.

2019-06-27 | GSE131396 | GEO

Systematic evaluation of RNA-Seq preparation protocol performance (RNASeq: TruSeq)

2019-06-27 | GSE131397 | GEO

Gene expression after deletion of Bmp4 in the mouse optic vesicle

Project description:Bmp4 was conditionally deleted from the mouse optic vesicle with Rx-Cre. The heads of wild type and knockout E10.5 mouse embryos were laser micodissected to isolate the lens ectoderm and prospective retina from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN Ovation Pico WTA system V2 kit. cDNA was biotinylated and hybridized to Illumina Mouse6 V2 bead arrays.

2015-02-20 | GSE62536 | GEO

mRNA profiling of Asns-silenced murine 4T1-T breast cancer cells grown in the presence and absence of Asparagine

Project description:Murine 4T1-T breast cancer cells were infected with an shRNA targeting Asparagine Synthetase (Asns) and grown in DMEM +/- asparagine. Cells were harvested and processed with the NuGen Ovation RNAseq system V2. Libraries were sequenced on an Illumina platform and mapped using Bowtie2 to the mm10 genome prior to transcript quantification using HT-Count.

2018-02-07 | GSE104964 | GEO

mRNA Profiling of Murine 4T1 Breast Cancer Cells with Asns knocked down

Project description:Murine 4T1-T Breast cancer cells were infected with retroviral vectors harboring shRNAs for murine or a Renilla, as negative control. After selection cells were harvested and processed with the NuGen Ovation RNAseq system V2. Libraries were sequenced on an Illumina platform and mapped using Bowtie2 to the mm10 genome prior to transcript quantification using HT-Count.

2018-02-07 | GSE104967 | GEO

GRN knockout, sorted brain cells

Project description:1 year old mice were perfused and brains were dissociated. Cells were fixed, immunolabeled and FACS sorted. RNA was extracted from neuron, astrocyte, and microglial cell populations. Typical RIN=4-5 for neurons, 6-8 for astrocytes, and 5-7 for microglia. Typical RNA yields ~100ng for neurons, ~20ng for microglia, and ~10ng for astrocytes. cDNA was generated from up to 25 ng of total RNA using Nugen’s RNA-Seq method for low-input RNA samples, Ovation RNA-Seq System V2 (NuGEN). (Per manufacturers instructions, total RNA was neither depleted of rRNA nor polyA-selected.) 1 μg of sheared cDNA was taken into further processing, starting at end repair step, using Illumina’s TruSeq RNA Sample Preparation Kit v2 (Illumina). The "SAMID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0007717

2017-07-06 | GSE78747 | GEO

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