Download nCounter® Virtual Cell Cycle Gene Set

Product Data Sheet
nCounter® Virtual Cell Cycle Gene Set
Product Highlights
•Simple
No more days spent cross referencing
databases
•Highly curated
Our expert bioinformaticists use a very
rigorous process to select the most
meaningful set of genes
•Efficient
Multiplexed assay profiles 183 cell
cycle-related genes in one reaction
•Cost-effective
Gold-standard data at a fraction of the
cost
A Gene Set You Can Count On
The nCounter Virtual Cell Cycle Gene Set is a
comprehensive list of 183 human genes known
to be differentially expressed in various phases
of the cell cycle. The gene list spans a broad
range of cell cycle-related biological processes,
including:
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•
•
•
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cell proliferation and differentiation
transcriptional regulation
oncogenesis
tumor suppression
DNA metabolism, replication and repair processes
The nCounter Virtual Cell Cycle Gene Set,
takes the guesswork out of gene selection
allowing researchers to accelerate their research
and quickly generate expression data for a large
panel of cell cycle-related genes.
The gene list was compiled by querying several
public databases for cell cycle-related genes.
This list was refined using multiple criteria,
including scoring each gene for relevance
in cell cycle-related pathways using IPA (by
Ingenuity® Systems, Inc). Each gene was also
verified to be differentially expressed in various
System Performance
Critical Specifications
Level of
Multiplexing
Recommended Amount of
Starting Material
Sample Types Supported
Reaction Volume
Limit of Detection
Fold Change Sensitivity
Spike Correlation
Linear Dynamic Range
Controls
183 genes known to be differentially expressed in cell
cycle
100ng of total RNA, or lysate from ~10,000 cells
Total RNA, Cell Lysates in GITC, FFPE derived total
RNA and PAXgene lysed whole blood, Amplified RNA
30 µL
0.5fM spike-in control (~1 copy per cell); 90% of the
time
>1.5 fold (>5 copies per cell)
>2 fold change (>1 copy per cell)
R2 ≥ 0.95
7 X 105 Total Counts
6 positive and 8 negative in each reaction
Genes Included
ABL1
CCND3
CDK6
E2F4
MCM2
ORC5L
RAD51
TGFB2
ANAPC1
CCNE1
CDK7
E2F5
MCM3
ORC6L
RB1
TGFB3
CDKN1A
E2F6
MCM4
PCNA
RBBP8
TNXB
ANAPC10 CCNE2
ANAPC11
CCNG2
CDKN1B
EP300
MCM5
PIK3CA
RBL1
TP53
ANAPC2
CCNH
CDKN1C
ESPL1
MCM6
PIK3R1
RBL2
TP73
ANAPC4
CDAN1
CDKN2A
FBXW7
MCM7
PKMYT1 RBX1
TWIST1
ANAPC5
CDC14A
CDKN2B
FZR1
MDM2
PLK1
UBE2M
RELA
ANAPC7
CDC14B
CDKN2C
GADD45A
MNAT1
POLA2
RPA1
WEE1
ARF1
CDC14C
CDKN2D
GADD45B
MPEG1
POLE
RPA2
XPO1
RPA3
YWHAB
ARF3
CDC16
CFL1
GADD45G
MPL
POLE2
ATF6B
CDC2
CHEK1
GBA2
MRE11A
POLR1A RPS6KA1 YWHAE
ATM
CDC20
CHEK2
GSK3B
MYC
POLR1B SFN
YWHAG
ATR
CDC23
CREB3
HDAC1
MYT1
POLR1C SHH
YWHAH
POLR1D SKP1
BRCA1
CDC25A
CREB3L1 HDAC2
NACA
BUB1
CDC25B
CREB3L3 HDAC3
NACAP1 PRB1
SKP2
BUB1B
CDC25C
CREB3L4 HDAC4
NEDD8
PRIM1
SMAD2
BUB3
CDC27
CREBBP
HDAC5
NEK1
PRIM2
SMAD3
CCNA1
CDC34
CUL1
HDAC6
NFKB1
PRKDC
SMAD4
YWHAQ
YWHAZ
CCNA2
CDC45L
DBF4
HDAC8
NFKBIA
PTCH1
SMC1A
CLTC*
CCNB1
CDC6
DHFR
JUN
NXT1
PTPRA
TBC1D8
GAPDH*
CCNB2
CDC7
DTX4
MAD1L1
ORC1L
PTTG1
TBX2
GUSB*
CCNB3
CDH1
E2F1
MAD2L1
ORC2L
PTTG2
TFDP1
HPRT1*
CCND1
CDK2
E2F2
MAD2L2
ORC3L
RAC1
TFDP2
PGK1*
CCND2
CDK4
E2F3
MAPK8
ORC4L
RAD50
TGFB1
TUBB*
phases of the cell cycle. The verification was
done using MSigDB, a repository of gene
expression data developed by researchers at the
Massachusetts Institute of Technology and the
Broad Institute Inc (Subramanian, Tamayo, et
al., 2005, PNAS 102, 15545-15550.). Other
public databases were used to obtain functional
gene expression information for each gene.
The final nCounter Virtual Cell Cycle Gene Set
consists of 183 cell cycle-related genes and six
internal reference genes. For the gene list and
additional information about this gene set, visit
the nCounter Virtual Panels product page at
www.nanostring.com.
Nanostring acknowledges Ingenuity® Systems,
Inc. (www.ingenuity.com) pathway tools
used in the development of the gene list and
supporting biological and chemical content.
nCounter® Analysis System Overview
The nCounter® Analysis System from
NanoString offers a cost-effective way to
easily profile hundreds of gene transcripts
simultaneously with high sensitivity and
precision. The digital detection of target
molecules and high levels of multiplexing
eliminate the compromise between data quality
and data quantity, bringing better sensitivity,
reproducibility, and linearity to your results. It
is ideal for studying defined gene sets across
a large sample set, e.g., microarray validation,
pathway analysis, biomarker validation, and
splice variation analysis.
The system utilizes a novel digital technology
that is based on direct multiplexed measurement
of gene expression and offers high levels of
precision and sensitivity (<1 copy per cell).
The technology uses molecular “barcodes”
and single molecule imaging to detect and
count hundreds of unique transcripts in a single
reaction.
*Internal Reference Genes
Ordering Information
Description
Quantity/Use
P/N
nCounter Virtual Cell Cycle Gene Set
48 Assays
96 Assays
192 Assays
384 Assays
GXA-VCC1-048
GXA-VCC1-096
GXA-VCC1-192
GXA-VCC1-384
nCounter Master Kit
All reagents, sample cartridges, and consumables
necessary for processing 48 or 192 assays.
48 Assays
192 Assays
NAA-AKIT-048
NAA-AKIT-192
NanoString Technologies, Inc.
530 Fairview Ave N, Suite 2000
Seattle, Washington 98109
(206) 378­-NANO • (206) 378­-6266
www.nanostring.com
© 2009-2010 NanoString Technologies, Inc. All rights reserved.
NanoString Technologies, NanoString, nCounter, and Molecules That Count are trademarks of NanoString Technologies, Inc., in the United States and/or other countries.
All other trademarks and/or service marks not owned by NanoString that appear in this product data sheet are the property of their respective owners.
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