Download Gene Expression and DNA Copy Number Analysis in Plants

Gene Expression and DNA Copy
Number Analysis in Plants
Gene Expression and DNA Copy
Number Analysis in Plants
QuantiGene® Plex Assay
Use for quantitative analysis of both multiplexed
gene expression and DNA copy number variation.
Sample types
Applications
Plant tissues, root, stem
branch, leaves, seeds
Plant breeding
Protoplasts
Identification of transgenic,
knockout, siRNA
Cultured cells
Zygosity testing
Isolated DNA/RNA
GMO testing
Many others
Viral, fungal, and bacterial testing
QuantiGene Plex Assays combine branched DNA signal amplification
technology and xMAP® (multi-analyte profiling) beads from Luminex®
to enable simultaneous direct quantification of multiple RNA or DNA
targets from a variety of sample types. bDNA technology is a sandwich
nucleic acid hybridization assay that provides a unique approach to
RNA and DNA detection and quantification by amplifying the reporter
signal rather than the template By measuring the RNA or DNA at
the sample source, the assay avoids biases and variability inherent to
extraction and amplification of target sequences.
How QuantiGene® Plex Assays work
Sample
preparation
Target
hybridization
Luminex® beads
with Capture Probes
Signal
amplification
PreAmplifier
Amplifier
Incubate beads with
sample and probes
Detection
Streptavidin
phycoerythrin (SAPE)
Read signal using
a Luminex®
instrument
Label Probe
80 RNA or DNA targets
per well
Capture
Extenders (CE)
Lyse sample
and go
Hybridizations and
wash steps
Label
Extenders (LE)
Blocking
Probes (BL)
Lysate
(with target RNA
or DNA)
Lysate
(with target RNA
or DNA)
Features and benefits
Any gene, any species – Customers have utilized our QuantiGene Assays to measure gene expression and DNA copy
variation from wheat, corn, soybean, rice, tobacco, lettuce, potato, tomato, cherry tomato, Arabidopsis, and many others
Fast customization – if we do not have the gene(s) in stock, we can create your custom panel within 2 weeks
True multiplexing – Measure up to 80 genes of interest and housekeeping genes in the same well with no crossreactivity 96- or 384-well plate format with results in 1.5 days
No PCR – No RNA and DNA purification, no reverse transcription, no PCR amplification, and none of the associated artifacts
Standardized platform – 96-well plate format compatible with Luminex 100, 200, MagPix® and FlexMap3D® systems
Simple workflow – ELISA-like workflow for direct hybridization of transcripts to beads and transcript labeling
2
Gene Expression - Soybean
Expression of AtBBX32 in soybean affects
the transcript abundance of central
clock components near ZT 0. Levels of
both central clock components GmLCL2
(A) and GmTOC1 (B) were assayed
by quantigene RNA extraction and
expression analysis from V2 leaf tissue
harvested from soybean plants grown
in a controlled environment. Growth
chamber experiment was performed in
a 14:10 hour photoperiod (Light:Dark)
with 650 mE of light. p-values based on
the difference between both transgenic
lines and wildtype control. * p#0.05.
Where error bars are not visible they are
smaller than the data points. Reprinted
from Preuss SB, et al., Expression of the
Arabidopsis thaliana BBX32 gene in
soybean increases grain yield, PLoS ONE
7(2): e30717 (2012). doi:10.1371/journal.
pone.0030717.g003
DNA Copy Number - Lettuce
Results of the QuantiGene Plex DNA Assay
with different sample sources, including
purified genomic DNA (gDNA) as well as
lysates from seeds (seed) and leaves (leaf)
of a transgenic lettuce plant. Normalized
data with gene 10 are shown to indicate
the relative DNA ratio.
1.2
Normalized to gene 10
1
0.8
Mar gDNA 300 ng
0.6
Mar Seed 40 μl
0.4
Mar Leaf 40 μl
0.2
0
Gene 1
Gene 2
Gene 3
Gene 4
Gene 5
Gene 6
Gene 7
Gene 8
Gene 9
Gene 10
3
Specifications
Gene expression
Limit of Detection
≤1,000-2,000 transcripts/assay well
Limit of Quantitation
≤2,000-4,000 transcripts/assay well
Linear Dynamic Range
≥3.0 logs
Assay CV
≤15% intra-assay; ≤20% inter-assay
Compatible Sample Types
Cultured cells, plant tissue, protoplasts, purified RNA
Assay Format
96- or 384-well plate
Targets/well
3- to 80-plex for both gene expression
DNA Copy Number
Limit of Detection
≤10,000 copies/assay well
Limit of Quantitation
≤20,000 copies/assay well
Linear Dynamic Range
≥2.5 logs
Assay CV
≤ 5% intra-assay; ≤20% inter-assay
Compatible Sample Types
Cultured cells, plant tissue, protoplasts purified DNA
Assay Format
96 or 384 well plate
Targets/well
3-80 genes
References
Preuss, S.B., et al. Expression of the Arabidopsis thaliana BBX32 Gene in Soybean Increases Grain Yield, PLoS ONE 17 Feb 2012, 7(2): e30717
Armstrong, T.A., et al. Quantification of Transgene-Derived Double-Stranded RNA in Plants Using the QuantiGene Nucleic Acid Detection Platform, J. Agric. Food Chem., 2 Dec
2013, 61(51) : 12557–12564
Cui, C., et al. Determination of Target Gene Copy Number in Plants Using QuantiGene Branched DNA Technology, ASA-CSSA-SSSA International Annual Meeting, Nov, 14, 2006, #162-1
Custom panels
Custom panel sets are available for any gene and any species. Custom panels ranging from 3- to 80 plex can be designed
and shipped within 2 weeks. Customers simply provide Affymetrix with a gene list, RefSeq IDs, or DNA sequence.
eBioscience (US) Tel: +1-888-999-1371
Affymetrix, Inc. Tel: +1-888-362-2447
Tel: +1-858-642-2058
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Affymetrix UK Ltd. Tel: +44-(0)1628-552550
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[email protected]
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www.ebioscience.com Please visit our website for international distributor contact information.
For Research Use Only. Not for use in diagnostic or therapeutic procedures.
QG03548-1- PLF QGPPX Plant 0414
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Products may be covered by one or more of the following patents: U.S. Patent Nos. 5,445,934; 5,744,305; 5,945,334; 6,140,044; 6,399,365; 6,420,169; 6,551,817; 6,733,977; 7,629,164;
7,790,389 and D430,024 and other U.S. or foreign patents. Products are manufactured and sold under license from OGT under 5,700,637 and 6,054,270. Cyanine (Cy) dye conjugates are covered
by US Patent Nos. US5,569,587 and US5,627,027.