QIAGEN Website    Quick Order    Online Seminar    Contact    My Account
Home  >  Products  >  PCR Home  >  PCR Array  >  Array List  >  Rat Embryonic Stem Cells

Embryonic Stem Cells PCR Array

Note: This RT² Profiler™ PCR Array was upgraded on March 1, 2013. This upgrade changed certain genes on this array and the catalog number changed from the 'Z' version to the 'Y' version. The 'Z' version of this array can be ordered by calling our Technical Support Group at 1-888-503-3187. The 'Z' version will be discontinued on September 30, 2013. To access the 'Z' version array, click here

Human Mouse Rat Other Species
 
Rat Embryonic Stem Cells PCR Array
The Rat Embryonic Stem Cell RT² Profiler™ PCR Array profiles the expression of 84 key genes involved in the maintenance of pluripotency and the self-renewal status of embryonic stem cells. Embryonic stem cells (ESC) hold great potential in treating diseases and injuries. However, turning them into a safe therapeutic agent still requires a deeper understanding how the control mechanisms for cell-lineage commitment and differentiation work. Some of this work is performed with ESCs, but similar studies make use of induced pluripotent stem cells (iPSC). The array includes embryonic stem cell-specific genes that maintain their pluripotent and self-renewal characteristics as well as key genes necessary for the first steps of iPSC generation. The array also includes differentiation markers that can be used to monitor the early events of ESC differentiation. A set of controls present on each array enables data analysis using the ΔΔCT method of relative quantification, assessment of reverse transcription performance, genomic DNA contamination, and PCR performance. Using real-time PCR, research studies can easily and reliably analyze expression of a focused panel of genes involved in embryonic stem cells maintenance and differentiation with this array.

The RT² Profiler™ PCR Arrays are intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.

96-well Plate, 384-well Plate and 100-well Disc formats are available.

Protocol Guide

 

Functional Gene Grouping How It Works Manual & Resources Reagents & Software
 
Pathway Source References    Modify this Array     Gene Table

Embryonic Stem Cell (ESC) Specific Genes:
Markers: Alpl, Gdf3 (Vgr2), Tdgf1, Tert.
Chromatin Regulators: Chd1, Chd7, Dnmt3b, Kat5.
Cofactors: Cnot3, Nr0b1, Paf1, Trim28.
Transcription Factors: Esrrb, Gbx2, Klf4, Lin28a, Myc, Nanog, Pou5f1 (Oct4), Smad1, Smad2, Smad3, Sox2, Stat3, Tbx3, Tcf7l1, Thap11, Utf1, Zfx.
Other Genes: Lefty1, Nodal.

Pluripotency: Aicda, Ccna2, Cdc42, Cdk1 (Cdc2), Dppa2, Dppa3, Fgf2 (bFGF), Foxd3, Hspa9, Mybl2, Nr5a2, Nr6a1, Otx2, Rif1, Scn1a, Sox15, Tcl1a, Zfp42.

iPSC Genes/Enhancers: Aicda, Klf4, Lin28a, Myc, Nanog, Pou5f1 (Oct4), Sox2, Utf1.

Germ Layers:
Ectoderm: En2, Fgf5, Meis1, Ncam1, Pax6.
Mesoderm: Des, Hand1, Mesp1, Mixl1, Myod1, T (Brachyury).
Endoderm: Gata1, Gata6, Gsc, Hnf4a, Sox17, Sox7.

Early Cell Types:
Neural Progenitors: Gfap, Nes, Olig2.
Cardiac Progenitors: Isl1, Nkx2-5.
Early Smooth Muscle Cells: Acta2, Tagln.
Hematopoietic Stem Cells/Early Endothelial Cells: Etv2, Flii, Gata2, Tal1, Tek (Tie2).
Mesenchymal Stem Cells: Cd44, Eng (Evi1), Nt5e, Thy1.
Hepatic Tissue: Alb, Tat.

Pathway Source References    Modify this Array     Gene Table
 

Functional Gene Grouping How It Works Manual & Resources Reagents & Software
 

"If you have access to a real-time PCR instrument, you can use PCR Arrays"

RT² Profiler™ PCR Arrays are the most reliable and sensitive gene expression profiling technology for analyzing a panel of genes in signal transduction pathways, biological process or disease related gene networks. The PCR Arrays can be used for research on cancer, immunology, stem cells, toxicology, biomarker discovery and validation, and phenotypic analysis of cells and transgenic animals. See the complete list of PCR Arrays.

You can use any 96-well or 384-well real-time PCR instrument. See instrument-specific setup instructions. Click below for detailed information.

How it Works

Performance Data

Application Data

How Biomarker Signature Genes were developed

Pathway Activity Score

How it Works

The PCR Arrays are sets of optimized real-time PCR primer assays on 96-well plate, 384-well plate, or 100-well disc for pathway or disease focused genes as well as appropriate RNA quality controls. The PCR array performs gene expression analysis with real-time PCR sensitivity and the multi-gene profiling capability of a microarray. Simply mix your cDNA template with the appropriate ready-to-use PCR master mix, aliquot equal volumes to each well of the same PCR Array, and then run the real-time PCR cycling program. (Download user manual)

1


Figure 1:

How RT² Profiler™ PCR Arrays Work - Protocol Chart

What it offers?
     Guaranteed Performance* - ready-to-use for gene expression analysis
     Time and cost saving - less than 30 min hands-on time for analyzing 84 genes and pathway activity
     Ease of data analysis using our easy-to-use web-based analysis tool

Layout and Controls: The PCR Arrays are available in 96-well plate, 384-well plate, and 100-well disc formats, and are used to monitor the expression of 84 genes related to a disease state or pathway including 16 experimentally derived Pathway Signature Biomarker genes plus five housekeeping genes. Controls are also included on each array for genomic DNA contamination, RNA quality, and general PCR performance.
You can easily perform a PCR Array experiment in your own laboratory, or send your samples to us and take advantage of our PCR Array Services.
*: when using complete PCR array system.

How Biomarker signature genes were developed

RT� Predictor PCR arrays have the capability to measure pathway activity based on target gene expression changes using SYBR Green real-time PCR technology. The algorithm developed along with individual RT� Predictor PCR array will measure pathway activity based on selected target gene expression changes and provide a single score of pathway activity readout to customer.

The target genes (Biomarker Signature genes) that will be used to measure pathway activity are experimentally derived and verified. These Biomarker Signature genes and companion algorithm are derived from a training data set consisting of 10-15 different cell lines whose pathway activity are either activated or inhibited with experimentally verified methods. The general workflow for Biomarker Signature gene development is illustrated below.

 


1

Development of Biomarker Signature genes for pathway activity determination

1
Development of Biomarker Signature genes for cellular toxicity determination

Pathway activity score:

Our unique algorithms use Ct values generated from the biomarker signature genes to generate the pathway activity score.

A 1

B 1

Interpretation of pathway activity score. (A) Signal transduction pathway activity. Positive score indicates stimulation of pathway activity while negative score indicates repression of pathway activity. * Samples with P value <0.05 as well as probability score >0.3 or <-0.3 indicate significant pathway activity change in an experimental sample compared to a control sample. (B) Cellular toxicity levels. *Samples with P value <0.05 and probability score >0.3 indicate significant toxicity level change in an experimental sample compared to a control sample.

Performance Data Sensitivity:
The complete PCR Array System yields a greater-than 85 percent present call with as little as 25 ng for gene expression profiling and as much as 5 �g of total RNA from a pathway representing genes expressed at a lower level.

Description: http://sabiosciences.com/images/SENSITIVITY_graph_508.jpg


Figure 2:

PCR Arrays Let You See More Genes with Less RNA
Different amounts of universal total RNA were characterized using QIAGEN�s PCR Array, and the percentage of detectable genes was calculated for each RNA amount.
As little as 25 ng total RNA yields greater than an 80% positive call.

Reproducibility

The complete PCR Array System demonstrates strong correlations across technical replicates, lots, and instruments with average correlation coefficients > 0.99 insuring reliable detection of differences in expression between biological samples.

Description: http://sabiosciences.com/images/REPRODUCIBILITY_graphs_508.jpg

 

050825_1 

050825_2 

050825_3 

050825_4

060111_1

0.993

0.989

0.995

0.992

060111_2

0.994

0.990

0.995

0.992

060111_3

0.992

0.990

0.993

0.992

060111_4

0.993

0.992

0.994

0.992

Figure 3:

PCR Arrays Yield Highly Reproducible Results
Four replicate sets of raw threshold data (1-4) obtained by two different scientists (A & B) at two different times (050825 & 060111) on Rat Drug Metabolism RT� Profiler™ PCR Arrays are directly compared. The results demonstrate a high degree of correlation (R2 > 0.990).

Specificity

The complete PCR Array System, with high quality input RNA, is guaranteed to yield single bands of the predicted size without primer dimers or other secondary products thus providing the most accurate real-time PCR results possible.

Description: http://sabiosciences.com/images/SPECIFICITY_graphs_508.jpg


Figure 4:

PCR Arrays Amplify A Single Gene-Specific Product in Every Reaction.
Universal total RNA was characterized on the TGF� / BMP Signaling Pathway PCR Array, followed by dissociation (melt) curve analysis. PCR Arrays specifically detect individual genes despite the expression of related gene family members in the same RNA sample.

 

Application Example

RT² Profiler™ PCR Arrays can be used in all areas of life science and biomedical research including:

  • Cancer
  • Inflammation and cytokine profiling
  • Stem cells
  • Neuroscience
  • Cell development
  • Signal transduction pathways
  • Biomarker screening and validation

We list below an example of application data generated by our R&D group. < /p>

Benefit of coupling gene profiling with activity determination

Rat embryonic colon epithelial FHC cells were treated with WNT3a ligand for 3h. Western blot analysis (A) indicated activation of WNT/b-catenin pathway activity while whole genome microarray study (B) suggested no change after Wnt3a treatment.

A B
1     1

 

 

To explain this discrepancy, RT² Profiler WNT Signaling PCR Array was used to exam pathway activity of and gene expression changes in the WNT/b-catenin pathway. Pathway activity score indicated no change in pathway activity in FHC cells after WNT3a treatment (C)

 

C

1

However, Gene expression profiling indicated upregulation of AXIN2, a negative regulator of WNT signaling, in FHC cells upon WNT3a treatment (D), suggesting a negative feedback mechanism to suppress pathway activity in FHC cells after WNT3a stimulation.

 

D

1

Cross Validation

The utility of the 16 Wnt/β-catenin signature genes was verified by cross validation with a Random Forest classification method and more than 80% of treatment samples were classified correctly based on this 16 gene signature, as shown below. Stimulated samples, different cell lines with pathway activity stimulated. Repressed samples, different cell lines with pathway activity repressed. Control samples, different cell lines without treatment.

Back to Top

 

Functional Gene Grouping How It Works Manual & Resources Reagents & Software
 
User Manual RT² Profiler™ PCR Array User Manual (PDF)
White Paper PCR Array: A Simple and Quantitative Method for Gene Expression Profiling (PDF)

PCR Array Application Examples: Toxicology, Oncology, and Immunology Research (PDF)

Data Analysis Free PCR Array Data Analysis Software (Web & Excel based)
Instrument Setup Instructions Materials & Equipment Required for our PCR products

PCR Array Instrument Setup Instructions & Protocol Files

FAQ FAQ about Real-Time PCR and Troubleshooting for our PCR products
Web Seminars Attend a live on-line seminar hosted by an Applications Scientist about PCR
Technical Brochures PCR Array Brochure (PDF)

Primer Assay Brochure (PDF)

SYBR Green Master Mix Brochure (PDF)

Powerpoint Presentations PCR Technology Overview Presentations
Citations &
Publications
Literature Citations using our PCR product
Pathway Central Pathway reviews and presentation-ready pathway maps
shRNA PlasmidsPathway related gene knockout - guaranteed > 70% knockdown
Individual PrimersValidated and Certified qPCR Primers for the genes on this array
Back to Top
 

Functional Gene Grouping How It Works Manual & Resources Reagents & Software
 

The complete RT² Profiler™ PCR Array System insures that you will get good results from your pathway-focused gene expression analysis experiment the first time, and every time guaranteed.

The Complete RT² Profiler™ PCR Array System Includes:

Our convenient and high-quality real-time RT-PCR accessory products complete the RT² Profiler™ PCR Array System and the RT² PCR Primer Assays. The other components needed for real-time PCR analysis are SYBR Green PCR master mix, first strand synthesis kit, and an optional RNA QC array.

Other recommended accessory products

NEW: RT² RNA QC PCR Array
Tests for RNA Quality and Inhibitors of RT-PCR Analyses, optional

Back to Top