Roche NimbleGen | Kits & Consumables

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
05993776001	NimbleGen Labeling and Hybridization Control Kit	CGH (2.1M, 3x720K, and 12x135K Arrays) CGX-6 & CGX-12 Arrays
05583683001	NimbleGen Hybridization Kit	CGH ChIP-chip DNA Methylation Gene Expression
05583934001	NimbleGen Hybridization Kit, LS	CGH ChIP-chip DNA Methylation Gene Expression
05327695001	Hybridization System Accessory Kit	CGH ChIP-chip DNA Methylation Gene Expression
05223512001	NimbleGen Sample Tracking Control Kit	CGH Gene Expression
05584507001	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

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

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 Nonamers¹	3	Yellow	11 O.D.
Cy5-Random Nonamers¹	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

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 Nonamers¹	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.

Labeling and Hybridization Control Kit NEW!

The NimbleGen Labeling and Hybridization Control (LHC) Kit contains two control DNA molecules, LHC-1 and LHC-2, for monitoring sample labeling and hybridization in dual-color comparative genomic hybridization (CGH) array experiments. The LHC Kit is designed for use with our Dual-Color DNA Labeling Kit on all current NimbleGen 2.1M, 3x720K, and 12x135K CGH arrays including NimbleGen cytogenetics CGX-6 and CGX-12 arrays.

The combination of this unique control kit and the compatible NimbleGen CGH arrays offers the following key benefits:

Unique Troubleshooting Tool: Monitor sample labeling and hybridization quality – determine if suboptimal experimental results are due to poor sample quality or unsuccessful labeling and hybridization steps, and spend less time troubleshooting poor quality samples.
Easy to Use: Follow standard NimbleGen CGH- array protocols and simply add LHC DNA controls to each DNA labeling reaction.
Integrated Analysis: LHC analysis is built into NimbleScan 2.6 software, enabling seamless reporting of LHC metrics and labeling and hybridization quality.
Cost Effective: Minimal additional cost added to each labeling reaction, but yielding a wealth of information.

Catalog Number

Name

Kit
Capacity

Kit
Components

05993776001

NimbleGen Labeling and Hybridization Control Kit

See Below

96 dual-color labeling reactions (96 Cy3 Test & 96 Cy5 Reference rxns)

Component	Vial Number	Cap Color	Quantity
LHC-1	1	White	200 µl
LHC-2	2	Yellow	200 µl
Storage Temperature for all components is -15°C to -25°C.

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.

Note: The catalog numbers for the NimbleGen Hybridization Kit and NimbleGen Hybridization Kit, LS have been updated. These kits contain the same formulations of highly optimized reagents as the previous kits.

Catalog Number

Name

Kit
Capacity

Kit
Components

05583683001

NimbleGen Hybridization Kit

See Below

Format^*	Number of Hybridizations	Number of Slides
2.1M	40	40
3x720K	102	34
12x135K	156	13
385K	100	100
4x72K	160	40
^* Not all applications are available in all formats.

Component	Vial Number	Quantity
2X Hybridization Buffer	1	1200µl
Hybridization Component A	2	500µl
Alignment Oligo	3	60µl
Storage temperature for all components is -15°C to -25°C.

05583934001

NimbleGen Hybridization Kit, LS

See Below

Format^*	Number of Hybridizations	Number of Slides
2.1M	122	122
3x720K	306	102
12x135K	480	40
385K	305	305
4x72K	488	122
^* Not all applications are available in all formats.

Component	Vial Number	Quantity
2X Hybridization Buffer	1	3 x 1200µl
Hybridization Component A	2	3 x 500µl
Alignment Oligo	3	3 x 60µl
Storage temperature for all components is -15°C to -25°C.

Hybridization System Accessory Kit

The hybridization system and accessory kit contains a verification assembly required to test that the hybridization system is mixing properly and replacement O-rings that can be used if the verification assembly shows a problem with the seal on the arrays. The kit also contains a disassembly tool, forceps and brayer which are required for use with NimbleGen arrays.

Catalog Number

Name

Components

05327695001

Hybridization System Accessory Kit

See Below

Component	Quantity
Hybridization System Disassembly Tool	1
Metal Forceps	1
Replacement O-Rings	6
Gasket Brayer	1
System Verification Assemblies	2

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 up to 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

Component¹	Part Number²	Storage Temperature³	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.

Note: The NimbleGen Wash Buffer kit has been updated to contain sufficient reagents to perform twice as many washes as the previous kit. Additionally, the DTT is now provided in powder form for improved stability during shipping. You can perform 20 washes, processing up to 12 slides per wash, with the components in the NimbleGen Wash Buffer kit.

Catalog Number

Name

Kit
Capacity

Kit
Components

05584507001

NimbleGen Wash Buffer Kit

See Below

Format	Number of Washes	Number of Slides
All	20	20 - 240

Component	Vial Number	Quantity
10X Wash Buffer I	1	2 x 540ml
10X Wash Buffer II	2	540ml
10X Wash Buffer III	3	540ml
DTT	4	2 x 185mg
Nuclease-Free Water	5	3 x 1000µl
Storage temperature for all components is +2°C to +8°C. Store DTT at -15°C to -25°C when reconstituted.

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 Container¹	8 (2 packages of 4)
¹ Washes one slide at a time.

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

Format	Number of Hybridizations	Number of Slides
2.1M	30	30
385K	60	60

Component	Storage Temperature¹	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

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
05223741001	10 Mixers
Name: NimbleGen HX3 Mixer Compatible Array Format: 3x720K

Catalog Number	Quantity
05223750001	10 Mixers
Name: NimbleGen HX12 Mixer Compatible Array Format: 12x135K

Catalog Number	Quantity
05223768001	10 Mixers
Name: NimbleGen X1 Mixer Compatible Array Format: 385K

Catalog Number	Quantity
05223725001	10 Mixers
Name: NimbleGen X4 Mixer Compatible Array Format: 4x72K

Catalog Number	Quantity
05223733001	10 Mixers