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NimbleGen Kits & Consumables

Figure 1. Workflow for CGH, ChIP-chip, DNA Methylation and Gene Expression arrays. For Sequence Capture workflow, visit the Sequence Capture page.

Roche NimbleGen provides an integrated solution for your genomics research needs, including microarrays, kits, consumables, instruments, software, and training. Together with the robust protocols provided for every step of your microarray analysis, from sample labeling to data analysis (Figure 1), these optimized reagents will enable you to conveniently and efficiently achieve the same high quality data in your own laboratory as that provided by the NimbleGen microarray service lab.

For our new Sequence Capture for Delivery product, we offer two kits for processing Sequence Capture arrays in your own lab. These kits allow efficient and convenient hybridization, washing, and elution of target DNA fragments for sequencing.

Ordering Information
Catalog Number Name Compatible Applications
05223547001 NimbleGen Dual-Color DNA Labeling Kit CGH
ChIP-chip
DNA Methylation
05223555001 NimbleGen One-Color DNA Labeling Kit Gene Expression
05223474001 NimbleGen Hybridization Kit CGH
ChIP-chip
DNA Methylation
Gene Expression
05223482001 NimbleGen Hybridization Kit, LS CGH
ChIP-chip
DNA Methylation
Gene Expression
05223512001 NimbleGen Sample Tracking Control Kit CGH
Gene Expression
05223504001 NimbleGen Wash Buffer Kit CGH
ChIP-chip
DNA Methylation
Gene Expression
05223539001 NimbleGen Array Processing Accessories CGH
ChIP-chip
DNA Methylation
Gene Expression
05340721001 NimbleGen Sequence Capture Hybridization Kit Sequence Capture
05340730001 NimbleGen Sequence Capture Wash and Elution Kit Sequence Capture
DNA Labeling Kits  NEW!
Dual-Color Labeling Kit

The NimbleGen Dual-Color (shown above) and One-Color DNA Labeling kits are designed for convenient and efficient labeling of DNA samples prior to hybridization to NimbleGen microarrays for CGH (Dual-Color), ChIP-chip (Dual-Color), DNA Methylation (Dual-Color), and Gene Expression (One-Color) analyses. These kits are based on Cy3- or Cy5-random priming and use a high concentration of exo- Klenow, lacking 3’ -> 5’ exonuclease activity, to incorporate dNTPs while replicating the DNA. This optimized protocol leads to high sample labeling yields and robust microarray performance. When used in combination with the NimbleGen Hybridization and Wash Buffer kits, the DNA Labeling kits ensure high signal-to-noise ratios and highly sensitive signals for NimbleGen microarray applications.

Catalog Number Name Kit
Capacity		 Kit
Components
05223547001 NimbleGen Dual-Color DNA Labeling Kit See Below See Below
Each Dual-Color labeling kit provides sufficient reagents for 10 Cy3 labeling reactions and 10 Cy5 labeling reactions. For all applications and platforms available one labeling reaction (of Cy3 and Cy5) is sufficient per hybridization, except for the ChIP-chip 2.1M format, where up to 3 labeling reactions are needed per hybridization.
Component Vial Number Cap Color Quantity
Nuclease-free Water 1 Clear 2 x 1,000µl
Random Primer Buffer 2 Brown 1,000µl
Cy3-Random Nonamers 1 3 Yellow 11 O.D.
Cy5-Random Nonamers 1 4 Green 11 O.D.
Klenow Fragment (3'->5' exo-) 50U/µl 5 Red 50µl
10mM dNTP Mix 6 Purple 250µl
Stop Solution (0.5M EDTA) 7 White 230µl
5M NaCl 8 Blue 250µl
Storage Temperature for all components is -15°C to -25°C.
1 Store in the dark.
05223555001 NimbleGen One-Color DNA Labeling Kit See Below See Below
Each One-Color labeling kit provides sufficient reagents for 20 Cy3 labeling reactions. For all Gene Expression microarray platforms available, one labeling reaction is sufficient per hybridization.
Component Vial Number Cap Color Quantity
Nuclease-free Water 1 Clear 2 x 1,000µl
Random Primer Buffer 2 Brown 1,000µl
Cy3-Random Nonamers 1 3 Yellow 22 O.D.
Klenow Fragment (3'->5' exo-) 50U/µl 4 Red 50µl
10mM dNTP Mix 5 Purple 250µl
Stop Solution (0.5M EDTA) 6 White 230µl
5M NaCl 7 Blue 250µl
Storage Temperature for all components is -15°C to -25°C.
1 Store in the dark.
Hybridization Kits

NimbleGen Hybridization Kit and NimbleGen Hybridization Kit, LS contain the necessary components for sample hybridization to NimbleGen arrays. The kits are designed specifically for NimbleGen CGH, ChIP-chip, DNA Methylation, and Gene Expression microarray applications.

The NimbleGen Hybridization kits incorporate a set of highly optimized hybridization reagents to ensure high signal-to-noise ratios and high sensitivity hybridization for all NimbleGen microarray applications. The proprietary hybridization buffer was formulated to maximize stringent signal strength without sacrificing specificity. The kits include a control Alignment Oligo that hybridizes to grid alignment features included on all NimbleGen arrays.

The number of hybridizations you can perform using a NimbleGen Hybridization Kit depends on the format of the microarrays (single or multiplex) to which samples are being hybridized.

Catalog Number Name Kit
Capacity		 Kit
Components
05223474001 NimbleGen Hybridization Kit See Below See Below
Format* Number of Hybridizations Number of Slides
2.1M 40 40
3x720K 102 34
12x135K 120 10
385K 100 100
4x72K 160 40
* Not all applications are available in all formats.
Component Storage
Temperature 1		 Quantity Volume per Tube
2X Hybridization Buffer 4°C 1 1.20ml
Hybridization Component A 4°C 1 0.5ml
Alignment Oligo 2 -20°C 3 1 55µl
1 Components in the kit require storage at differing temperatures. Upon receipt of the kit, remove the components and store them at the recommended storage temperatures noted in the table above.
2 The Alignment Oligo is a mixture of Cy3- and Cy5-labeled 48mer oligonucleotides that hybridize to alignment features on NimbleGen arrays. It is required for proper extraction of array data from the scanned image.
3 The Alignment Oligo is labeled with Cy™ dyes and is sensitive to photobleaching and freeze-thawing. After thawing stock tubes for the first time, aliquot the Alignment Oligo into single-use volumes and freeze at -20°C. Protect tubes from light.
05223482001 NimbleGen Hybridization Kit, LS See Below See Below
Format* Number of Hybridizations Number of Slides
2.1M 120 120
3x720K 306 102
12x135K 480 40
385K 300 300
4x72K 480 120
* Not all applications are available in all formats.
Component Storage
Temperature 1		 Quantity Volume per Tube
2X Hybridization Buffer 4°C 3 1.20ml
Hybridization Component A 4°C 3 0.5ml
Alignment Oligo 2 -20°C 3 3 55µl
1 Components in the kit require storage at differing temperatures. Upon receipt of the kit, remove the components and store them at the recommended storage temperatures noted in the table above.
2 The Alignment Oligo is a mixture of Cy3- and Cy5-labeled 48mer oligonucleotides that hybridize to alignment features on NimbleGen arrays. It is required for proper extraction of array data from the scanned image.
3 The Alignment Oligo is labeled with Cy™ dyes and is sensitive to photobleaching and freeze-thawing. After thawing stock tubes for the first time, aliquot the Alignment Oligo into single-use volumes and freeze at -20°C. Protect tubes from light.
Sample Tracking Control Kit

The NimbleGen Sample Tracking Control Kit contains 12 Sample Tracking Controls (STCs). A unique STC is added to each sample before hybridization to a multiplex array, enabling you to confirm that the correct sample was hybridized to each array. The kit is designed specifically for NimbleGen CGH and Gene Expression multiplex microarray applications.

You can perform 480 hybridizations to 4x72K or 12x135K arrays with the components in the NimbleGen Sample Tracking Control kit.

Catalog Number Name Kit
Capacity		 Kit
Components
05223512001 NimbleGen Sample Tracking Control Kit See Below See Below
Format Number of Hybridizations Number of Slides
3x720K 300 100
12x135K 480 40
4x72K 480 120
Component 1 Part Number 2 Storage Temperature 3 Quantity Volume per Tube
Sample Tracking Control 1
Sample Tracking Control 3
Sample Tracking Control 5
Sample Tracking Control 7
Sample Tracking Control 9
Sample Tracking Control 11
Sample Tracking Control 13
Sample Tracking Control 15
Sample Tracking Control 16
Sample Tracking Control 17
Sample Tracking Control 18
Sample Tracking Control 20		 01012
01014
01016
01018
01020
01022
01024
01026
01027
01028
01029
01031		 -20°C 1 of each unique STC 140µl
1 Each STC is a Cy3-labeled 48mer oligonucleotide that hybridizes to sample tracking control probes on NimbleGen arrays.
2 Part numbers are provided for reference only. STCs cannot be purchased individually.
3 The STCs are labeled with Cy3™ dye and are sensitive to photobleaching and freeze-thawing. After thawing stock tubes for the first time, aliquot the STCs into single-use volumes and freeze at -20°C. Protect tubes from light.
Wash Buffer Kit

The NimbleGen Wash Buffer kit contains optimized buffers to ensure efficient washing of NimbleGen arrays after hybridization. The kit is designed specifically for NimbleGen CGH, ChIP-chip, DNA Methylation, and Gene Expression microarray applications.

You can perform 10 washes, processing up to 12 slides per wash, with the components in the NimbleGen Wash Buffer kit.

Catalog Number Name Kit
Capacity		 Kit
Components
05223504001 NimbleGen Wash Buffer Kit See Below See Below
Format Number of Washes Number of Slides
All 10 10 - 120
Component Storage Temperature 1 Quantity Volume per Tube
10X Wash Buffer I Room Temperature 1 500ml
10X Wash Buffer II Room Temperature 1 250ml
10X Wash Buffer III Room Temperature 1 250ml
1M DTT -20°C 1 1ml
1 Components in the kits require storage at differing temperatures. Upon receipt of the NimbleGen Wash Buffer kit, remove components and store them at the recommended storage temperatures.
Array Processing Accessories

NimbleGen Array Processing Accessories contain the necessary labware to use when washing NimbleGen arrays after hybridization. The accessories are designed specifically for NimbleGen CGH, ChIP-chip, DNA Methylation, and Gene Expression microarray applications.

Catalog Number Name Kit
Capacity		 Kit
Components
05223539001 NimbleGen Array Processing Accessories Unlimited See Below
Component Quantity  
Slide Rack 1
Wash Tank 4
Slide Container 1 8 (2 packages of 4)
1 Washes one slide at a time.
Array Re-Use Kits

These kits provide all the reagents required to gently but thoroughly remove previously hybridized sample from NimbleGen arrays without adversely affecting probe performance through additional rounds of hybridization. NimbleGen arrays may be used multiple times depending on the application and sample quality.

Note: NimbleGen does not guarantee array reuse. Array reuse is not recommended for Gene Expression arrays.

Catalog Number Name Number of Slides Components
Contact
Customer Service		 NimbleGen Array Reuse Kit 40 40 See Below
Component Quantity
Array Reuse Solution 2 x 500ml
Processing Tanks 2
Array Processing Racks 1
Slide Processing Containers 4
Contact
Customer Service		 NimbleGen Array Reuse Kit Refill 40 40 See Below
Component Quantity
Array Reuse Solution 2 x 500ml
Sequence Capture Kits

Use the NimbleGen Sequence Capture Hybridization Kit to perform up to 30 hybridizations (2.1M) or 60 hybridizations (385K) of fragmented gDNA libraries to a NimbleGen Sequence Capture array.

The NimbleGen Sequence Capture Wash and Elution Kit contains optimized buffers to ensure efficient washing of NimbleGen Sequence Capture arrays after hybridization. You can perform 15 elutions on 2.1M and 385K arrays with the components in one kit.

Catalog Number Name Kit
Capacity		 Kit
Components
05340721001 NimbleGen Sequence Capture Hybridization Kit See Below See Below
Format Number of Hybridizations Number of Slides
2.1M 30 30
385K 60 60
Component Storage Temperature 1 Quantity Volume per Tube
2X SC Hybridization Buffer 4°C 1 600µl
SC Hybridization Component A 4°C 1 250µl
1 The kit is shipped on blue ice (-20 ºC). Upon receipt of the kit, remove the components and store them at the recommended storage temperatures noted in the table above.
05340730001 NimbleGen Sequence Capture Wash and Elution Kit See Below See Below
Format Number of Washes/Elutions Number of Slides
2.1M 15 15
385K 15 15
Component Storage Temperature Quantity Volume per Tube
2X Stringent Wash Buffer Room Temperature 1 500ml
10X SC Wash Buffer I Room Temperature 1 50ml
10X SC Wash Buffer II Room Temperature 1 250ml
10X SC Wash Buffer III Room Temperature 1 50ml
Elution Reagent Room Temperature 2 25ml

For more information on NimbleGen Sequence Capture products, visit the Sequence Capture page.

Mixers

NimbleGen mixers, which you adhere directly to microarray slides before sample loading and hybridization, are a key component of the NimbleGen Hybridization System. The mixers allow for low hybridization volume, leading to greater sensitivity and reliable results while economizing on sample requirements. They fit NimbleGen arrays precisely and are optimized for NimbleGen array dimensions, ensuring uniform signal and high sensitivity with minimal sample volume.

NimbleGen Mixers
Name: NimbleGen HX1 Mixer
Compatible Array Format: 2.1M
Catalog Number Quantity
05391733001 5 Mixers
05223741001 10 Mixers
Name: NimbleGen HX3 Mixer
Compatible Array Format: 3x720K
Catalog Number Quantity
05391741001 5 Mixers
05223750001 10 Mixers
Name: NimbleGen HX12 Mixer
Compatible Array Format: 12x135K
Catalog Number Quantity
05391768001 5 Mixers
05223768001 10 Mixers
Name: NimbleGen X1 Mixer
Compatible Array Format: 385K
Catalog Number Quantity
05391717001 5 Mixers
05223725001 10 Mixers
Name: NimbleGen X4 Mixer
Compatible Array Format: 4x72K
Catalog Number Quantity
05391725001 5 Mixers
05223733001 10 Mixers
Literature

For a complete listing of literature covering all Roche NimbleGen products and services please visit our literature page.

  

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