After FACS sorting, total RNA was extracted, and the microarray probes were synthesized using the Ovation RNA amplification system (Nugen, San Carlos, CA) as previously described[3 (link)].
Ovation rna amplification system
Manufactured by Tecan
Sourced in United States
The Ovation RNA Amplification System is a laboratory equipment designed for the amplification of RNA samples. Its core function is to generate amplified RNA from a small amount of input RNA material, enabling subsequent analysis and applications.
Automatically generated - may contain errors
Lab products found in correlation
Encore biotin module, by Tecan (3 mentions)
Nucleospin rna 2 kit, by Macherey-Nagel (2 mentions)
Facsaria 3 cell sorter, by BD (2 mentions)
Genearray scanner 3000, by Thermo Fisher Scientific (1 mentions)
Human mirna microarray, by Agilent Technologies (1 mentions)
Genespring gx 12, by Agilent Technologies (1 mentions)
Fl ovation cdna biotin module v2, by Tecan (1 mentions)
Affymetrix human u133 plus 2.0 arrays, by Thermo Fisher Scientific (1 mentions)
Genechip human genome u133 plus 2.0 microarray, by Thermo Fisher Scientific (1 mentions)
2100 bioanalyzer, by Agilent Technologies (1 mentions)
Qiaquick pcr purification kit, by Qiagen (1 mentions)
Genechip mouse genome 430 2.0 array, by Thermo Fisher Scientific (1 mentions)
Nucleospin rna xs isolation kit, by Macherey-Nagel (1 mentions)
Hg u133 plus 2.0 array, by Thermo Fisher Scientific (1 mentions)
Tri reagent, by Molecular Research Center (1 mentions)
Bioanalyzer, by Agilent Technologies (1 mentions)
Rneasy ffpe kit, by Qiagen (1 mentions)
Mouse wg6 v2 beadchips, by Illumina (1 mentions)
Neon system, by Thermo Fisher Scientific (1 mentions)
Nanoluc luciferase, by Promega (1 mentions)
11 protocols using ovation rna amplification system
1
RNA Extraction and Microarray Probe Synthesis
2
RNA Amplification and Microarray Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Between 5 and 20 ng of total RNA from each PBMC sample was used to generate high-fidelity cDNA using an Ovation RNA amplification system (NuGEN Technologies, Inc., San Carlos, CA) according to the manufacturer’s protocol. The amplified cDNA was fragmented to 50 to 100 nucleotides, labeled with biotin, and hybridized to the Affymetrix GeneChip.HG-U219 high-density oligonucleotide array (Affymetrix, Santa Clara, CA). After hybridization, the arrays were stained with streptavidin-phycoerythrin and washed in an Affymetrix fluidics module using standard Affymetrix protocols. The detection and quantitation of target hybridization was performed using a GeneArray Scanner 3000 (Affymetrix). All procedures were performed at the Bionomics Research and Technology Center, Rutgers University, Piscataway, NJ.
3
Bladder Transcriptome Profiling by miRNA & mRNA Microarray
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Agilent Human miRNA Microarray (V3, based on Sanger miRbase release 12.0) was used for measuring miRNA expression in bladder samples. Samples used for the Agilent miRNA microarray were labelled as described by the manufacturer. Affymetrix Human U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA) were used for measuring gene expression in bladder samples. Samples used for Affymetrix microarray were amplified using the Ovation RNA Amplification System (NuGEN, San Carlos, CA, USA) and labelled using FL-Ovation cDNA Biotin Module V2 (NuGEN) following the manufacturer's protocol. Raw intensity miRNA data were normalised and median transformed using GeneSpring GX 12 (Agilent). The raw mRNA data were log transformed and analysed using Partek Genomics Suite 6.6 (Partek, Saint Louis, MO, USA). Only detected probe sets were used, and compromised or undetected probe sets were filtered out. One-way ANOVA and Tukey's honestly significant difference (HSD) post hoc test were performed across all samples to obtain miRNAs or mRNAs differentially expressed (P<0.05). Unsupervised hierarchical cluster analysis was performed on the list of differentially expressed probe sets with a fold change of ⩾2 (miRNAs) or a fold change of ⩾10 (mRNAs).
4
Affymetrix Microarray Expression Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was amplified, labeled and purified using the Ovation RNA amplification system (Nugen Technologies Inc., San Carlos, CA, USA). Microarray analysis was performed on Affymetrix GeneChip Human Genome U133 plus 2.0 microarray (Affymetrix Inc, Santa Clara, CA, USA) at the microarray core facility of Shanghai Biotechnology Corporation.
5
Transcriptomic Analysis of GC B-cells
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
B220+CD95+PNA+ GC B-cells were sorted from Kmt2dfl/fl, Kmt2dfl/+ and Kmt2d+/+ splenocytes (CD19-Cre or Cγ1-Cre; n = 3 mice/genotype) in a BD FacsAria III cell sorter (BD Biosciences). Total RNA was extracted using the NucleoSpin RNA II kit according to the manufacturer's instructions (MACHEREY-NAGEL) and, from each sample, 20 ng were reverse transcribed and amplified using the Ovation RNA Amplification System (NuGEN), followed by labeling with the Encore Biotin Module (NuGEN). Labeled samples were hybridized to Affymetrix MG430 2.0 arrays as recommended by the manufacturer. Raw expression values were normalized using the Robust Multiarray Averaging (RMA) algorithm in GenePattern (http://www.broadinstitute.org/cancer/software/genepattern/ )66 (link), and multiple probes corresponding to the same gene were collapsed to a single probe based on maximum t-statistic. Differentially expressed genes were determined by the Student's t-test using a FDR ≤ 0.15 (after Benjamini-Hochberg correction)67 and absolute fold change ≥ 1.5. The GEO accession number for these data is GSE67388. For visualization of gene-expression intensity, all gene expression data were normalized by gene (z-score transformation).
6
Transcriptome Analysis of GC B Cells
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Purified B cells were sorted from SRBC-immunized mice (day 7) into GFP+ and GFP− GC (CD95hiPNAhi) B cell fractions. Total RNA of ∼3 × 104 cells was isolated using the Nucleospin RNA XS isolation kit (MACHEREY-NAGEL) according to the manufacturer’s protocol, and RNA integrity >8 was determined on a BioAnalyzer 2100 (Agilent Technologies). Approximately 10 ng of total RNA was reverse transcribed into cDNA with the Ovation RNA Amplification System (NuGEN) according to the manufacturer’s instructions, followed by purification of the amplified cDNA using the QIAquick PCR purification kit (QIAGEN). 3 µg of total cDNA was labeled and fragmented using the Encore Biotin Module (NuGEN) and hybridized onto GeneChip Mouse Genome 430 2.0 arrays (Affymetrix). Data were analyzed using Affymetrix MAS5. Supervised analysis was performed with the GENES@WORK software platform as previously described (Klein et al., 2001 (link)). GEP data are available through the GEO database (GSE58839 ).
7
Transcriptome Analysis of Cryopreserved PBMCs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
RNA was prepared from dimethyl sulfoxide-cryopreserved PBMC samples using TRI Reagent and protocol (Molecular Research Center Inc., Cincinnati, OH, USA). The preparation, amplification, and labeling of copy DNA was performed using Ovation RNA Amplification System and protocol (NuGen Technologies, San Carlos, CA, USA). Gene expression levels were determined using Affymetrix HG-U133 Plus 2.0 arrays of 54,120 probe sets and protocol (Affymetrix, Santa Clara, CA, USA). The data were made publicly available via ArrayExpress under accession number E-MTAB-4629.
8
Laser-Guided Prostate Transcriptomics
9
Transcriptomic Analysis of GC B-cells
10
Transgenic Lrig1-EGFP-IRES-CreERT2 Mouse Model
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Lrig1-EGFP-IRES-CreERT2 mice were created via knock-in of an EGFP-ires-CreERT2 cassette into the endogenous Lrig1 locus in C57Bl/6 embryonic stem cells. For global gene-expression profiling, RNA from skin keratinocytes was isolated, pre-amplified (Ovation RNA Amplification System, NuGEN, Leeds, UK) and then hybridized to MouseWG-6 v.2 BeadChips (Illumina) [21 (link)].
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!