NimbleGen Systems, Inc.

Advantages of NimbleGen HD2 Arrays

More Probes Enable Increased Resolution and Cost-Effective Analysis

With 2.1 million probes, NimbleGen HD2 arrays offer the highest density microarray platform currently available for CGH and ChIP analysis. NimbleGen HD2 arrays enable genome-wide detection of copy number variation down to ~5 kb resolution (human) and transcription factor binding at 100bp resolution. Fewer HD2 arrays and less total sample are required to perform CGH fine-tiling or genome-wide ChIP-chip studies, which leads to a significant reduction in cost to perform such analyses.

Long Oligonucleotide Probes Enhance the Accuracy of Your Analysis

NimbleGen HD2 arrays utilize long oligo probes, which have been shown to provide increased sensitivity, specificity, and reproducibility. Depending on the specific array design, HD2 arrays are synthesized with oligos between 50 and 75 bases in length.

Only the Most Current Genomes

The inherent flexibility of the Roche NimbleGen technology enables the rapid creation of array designs using only the most current genomic sequence from any eukaryotic genome. NimbleGen HD2 arrays will deliver the highest resolution and highest quality CGH and ChIP-chip data on the latest genomic build.

NimbleGen HD2 Specifications

Total probes	2.1 million
Probe length	50 - 75mer (ChIP-chip) 60mer (CGH)
Feature size	13μm x 13μm
Array size	62mm x 14mm
Slide size	1” x 3” (25mm x 76mm) glass

CGH Analysis

Figure 1. Test and reference gDNA samples were independently labeled with fluorescent dyes, co-hybridized to a NimbleGen 2.1M (HD2) or 385K human whole-genome CGH array, and scanned using a 5μm scanner. Log₂-ratio data from the two platforms are displayed in the Roche NimbleGen SignalMap™ software in parallel to an annotation track showing known copy number variants (CNVs) from the Database of Genomic Variants (http://projects.tcag.ca/variation/). The increased probe density on the HD2 human whole-genome CGH array (1.1kb vs. 6kb median probe spacing) enabled the detection of a novel ~3kb CNV that was detected by only a single probe on the 385K platform (see arrows above). In addition, fine structure of a previously reported copy number variant region was further elucidated using the HD2 human whole-genome CGH array.

CGH HD2 Custom Arrays

Custom HD2 CGH	Single array/slide with 2,100,000 probes.
Source	Customer-defined
Build	Customer-defined
Probe Length	60mer
Probe Spacing	Uniform or mixed-density
Design Options	Custom tiling up to 2,100,000 probes per array. Single or multiple chromosomal regions per array. Single or multiple array designs.
Feature Size	13μm x 13μm
Array Size	62mm x 14mm
Overall Slide Dimensions	1" x 3" (25 x 75mm)
Recommended Storage	Store arrays desiccated at room temperature.

CGH HD2 Catalog Tiling Arrays

Homo sapiens (Whole Genome Tiling Array) New Design!

Source: UCSC Build: HG18, NCBI 36 Probe Length: 60mer Median Probe Spacing: 1169bp Platform: HD2 Probes per Array: 2,100,000 Feature Size: 13μm x 13μm Array Dimensions: 62mm x 14mm Overall Slide Dimensions: 1" x 3" (25 x 75mm) Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number	Design Name	Description	Version
B7074-00-01	HG18 WG Tiling 2.1M CGH v2.0D	Whole Genome Tiling Array	2.0D

ChIP-chip Analysis

Figure 2. Comparison of me3-H3K27 data obtained from the NimbleGen HD2 and 385K ChIP-chip platforms using a 5μm scanner. Data shown are within the H19/IGF2 cluster on chromosome 11. The increased probe coverage of the HD2 platform resulted in increased resolution of called peaks when compared to the 385K platform.

ChIP-chip HD2 Promoter Tiling Arrays

General Array Specs Probe Length: 50-75mer Platform: HD2 Probes per Array: 2,100,000 Feature Size: 13μm x 13μm Array Dimensions: 62mm x 14mm Overall Slide Dimensions: 1" x 3" (25 x 75mm) Recommended Storage: Store arrays desiccated at room temperature.
Organism: Homo sapiens * Source: UCSC Build: HG18
Catalog Number	Design	Promoter Upstream Tiling (bp)	Promoter Downstream Tiling (bp)	Number of CpG Islands	miRNA Promoters
C7291-00-01	HG18 Deluxe Promoter HX1	7250	3250	28226	475 (-15kb through mature transcript)
* Array includes probes tiling through biologically significant ENCODE regions (HoxA, β-globin, Apo, among others)
Organism: Mus musculus Source: UCSC Build: MM8
Catalog Number	Design	Promoter Upstream Tiling (bp)	Promoter Downstream Tiling (bp)	Number of CpG Islands	miRNA Promoters
C7244-00-01	MM8 Deluxe Promoter HX1	8200	3000	15963	249 (-20kb to 1kb)

ChIP-chip HD2 Whole-Genome Tiling Arrays

Caenorhabditis elegans

Source: UCSC Build: CE180 Probe Length: 50-75mer Median Probe Spacing: 40bp Platform: HD2 Probes per Array: 2,100,000 Feature Size: 13μm x 13μm Array Dimensions: 62mm x 14mm Overall Slide Dimensions: 1" x 3" (25 x 75mm) Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number	Design Name	Description	Chromosome	Tiling Start	Tiling Stop
C6781-00-01	CE180 Tiling Set HX1	Array 1 of 1	chr I	489	15,072,205
			chr II	321	15,279,085
			chr III	126	13,783,367
			chr IV	285	17,492,284
			chr V	331	20,919,326
			chr X	251	17,718,642

Drosophila melanogaster

Source: UCSC Build: DM5 Probe Length: 50-75mer Median Probe Spacing: 55bp Platform: HD2 Probes per Array: 2,100,000 Feature Size: 13μm x 13μm Array Dimensions: 62mm x 14mm Overall Slide Dimensions: 1" x 3" (25 x 75mm) Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number	Design Name	Description	Chromosome	Tiling Start	Tiling Stop
C7245-00-01	DM5 Tiling Set HX1	Array 1 of 1	chr 2L	5131	23,011,180
			chr2Lhet	2,538	367,898
			chr 2Rhet	11	3,288,675
			chr 2R	3036	21,146,403
			chr 3L	19,811	24,541,069
			chr 3Lhet	231	2,555,369
			chr 3R	6	27,898,700
			chr 3Rhet	1	2,517,409
			chr 4	1	1,347,833
			chr M	6	19,373
			chr U	2,051	10,048,502
			chr X	116	22,422,248
			chr Xhet	666	203,681
			chr Yhet	1	346,895

Homo sapiens

Source: UCSC Build: HG18 Probe Length: 50-75mer Median Probe Spacing: 100bp Platform: HD2 Probes per Array: 2,100,000 Feature Size: 13μm x 13μm Array Dimensions: 62mm x 14mm Overall Slide Dimensions: 1" x 3" (25 x 75mm) Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number	Design Name	Description	Chromosome	Tiling Start	Tiling Stop
C7257-SET-01	HG18Tiling Set HX1	10 Array Set	Whole Genome 10-Array Set
C7246-00-01	HG18Tiling Set 1 HX1	Array 1 of 10	chr1	505	247,195,005
C7246-00-01	HG18Tiling Set 1 HX1	Array 1 of 10	chr2	321	60,027,826
C7247-00-01	HG18Tiling Set 2 HX1	Array 2 of 10	chr2	6,002,792	242,951,119
C7247-00-01	HG18Tiling Set 2 HX1	Array 2 of 10	chr3	35,001	106,782,710
C7248-00-01	HG18Tiling Set 3 HX1	Array 3 of 10	chr3	106,782,825	199,501,827
			chr4	216	191,273,063
			chr5	64,925	2,304,112
C7249-00-01	HG18Tiling Set 4 HX1	Array 4 of 10	chr5	2,304,217	180,857,866
C7249-00-01	HG18Tiling Set 4 HX1	Array 4 of 10	chr6	5,001	111,919,925
C7250-00-01	HG18Tiling Set 5 HX1	Array 5 of 10	chr6	111,920,005	170,899,992
			chr7	49,317	158,821,424
			chr8	521	74,730,105
C7251-00-01	HG18Tiling Set 6 HX1	Array 6 of 10	chr8	74,730,205	146,274,826
			chr9	516	140,273,252
			chr10	1,773,517	101,402,412
C7253-00-01	HG18Tiling Set 7 HX1	Array 7 of 10	chr10	101,402,517	135,374,737
			chr11	62,725	134,452,384
			chr12	17,426	121,385,801
C7254-00-01	HG18Tiling Set 8 HX1	Array 8 of 10	chr12	121,385,901	132,349,534
			chr13	17,918,026	114,142,980
			chr14	18,070,206	106,368,585
			chr15	18,260,026	100,338,915
			chr16	23	6,248,313
C7255-00-01	HG18Tiling Set 9 HX1	Array 9 of 10	chr16	62,48,403	88,827,254
			chr17	16	78,774,742
			chr18	623	76,117,153
			chr19	11,316	63,811,651
			chr20	8,016	16,260,605
C7256-00-01	HG18Tiling Set 10 HX1	Array 10 of 10	chr20	16,260,705	62,435,704
			chr21	9,720,013	46,944,102
			chr22	14,430,026	49,590,821
			chrX	112	154,912,711
			chrY	112	57,771,911
			chr1 random	721	1,663,126
			chr2 random	21	185,401
			chr3 random	16	749,118
			chr4 random	16	842,224
			chr5 random	11	143,119
			chr6 random	26	1,875,407
			chr7 random	101	549,124
			chr8 random	16	943,723
			chr9 random	402	1,146,305
			chr10 random	6	112,020
			chr11 random	26	214,804
			chr13 random	6	186,723
			chr15 random	1	784,221
			chr16 random	6	105,409
			chr17 random	26	2,617,303
			chr18 random	16	4,126
			chr19 random	701	301,702
			chr21 random	1	1,679,604
			chr22 random	21	256,508
			chrX random	6	1,718,603

Homo sapiens - Economy

Source: UCSC Build: HG18 Probe Length: 50-75mer Median Probe Spacing: 205bp Platform: HD2 Probes per Array: 2,100,000 Feature Size: 13μm x 13μm Array Dimensions: 62mm x 14mm Overall Slide Dimensions: 1" x 3" (25 x 75mm) Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number	Design Name	Description	Chromosome	Tiling Start	Tiling Stop
C7262-SET-01	HG18 ECONOMY Tiling Set HX1	4 Array Set	Whole Genome 4-Array Set
C7258-00-01	HG18 ECONOMY Tiling Set 1 HX1	Array 1 of 4	chr1	1,313	247,195,565
			chr1 random	1,611	1,662,469
			chr2	2,201	242,751,149
			chr2 random	21	185,571
			chr3	35,003	199,434,305
			chr3 random	1	749,178
			ch4	6,126	44,383,123
C7259-00-01	HG18 ECONOMY Tiling Set 2 HX1	Array 2 of 4	chr4	44,382,481	191,260,303
			chr4 random	1	842,414
			chr5	64,884	180,837,023
			chr5 random	230	141,377
			chr6	5,003	170,896,992
			chr6 random	443	1,875,467
			chr7	34,003	158,821,318
			chr7 random	68	547,255
			chr8	1	72,911,264
C7260-00-01	HG18 ECONOMY Tiling Set 3 HX1	Array 3 of 4	chr8	72,910,390	146,273,068
			chr8 random	621	943,633
			chr9	1,577	140,269,382
			chr9 random	1,152	1,146,350
			chr10	50,003	135,372,404
			chr10 random	1	113,198
			chr11	50,003	134,450,777
			chr11 random	1	214,910
			chr12	17,432	132,289,534
			chr13	17,918,003	114,127,903
			chr13 random	1	186,321
			chr14	18,126,854	41,598,996
C7261-00-01	HG18 ECONOMY Tiling Set 4 HX1	Array 4 of 4	chr14	41,599,466	106,360,585
			chr15	18,303,913	100,337,245
			chr15 random	1	784,131
			chr16	1,145	88,820,562
			chr16 random	487	105,389
			chr17	1	78,654,674
			chr17 random	1	2,617,421
			chr18	1,148	76,116,178
			chr18 random	1	4,020
			chr19	11,003	63,806,013
			chr19 random	8,248	301,762
			chr20	8,003	62,432,795
			chr21	9,734,029	46,941,590
			chr21 random	1	1,679,594
			chr22	14,430,003	49,590,901
			chr22 random	1	256,573
			chrM	1	16,340
			chrX	449	154,911,455
			chrX random	1	1,718,581
			chrY	449	57,770,655

Mus musculus

Source: UCSC Build: MM8 Probe Length: 50-75mer Median Probe Spacing: 100bp Platform: HD2 Probes per Array: 2,100,000 Feature Size: 13μm x 13μm Array Dimensions: 62mm x 14mm Overall Slide Dimensions: 1" x 3" (25 x 75mm) Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number	Design Name	Description	Chromosome	Tiling Start	Tiling Stop
C7273-SET-01	MM8Tiling Set HX1	10 Array Set	Whole Genome 10-Array Set
C7263-00-01	MM8Tiling Set 1 HX1	Array 1 of 10	chr1	3,000,001	197,069,505
			chr1 random	122	172,060
			chr2	3,006,249	65,850,316
C7264-00-01	MM8Tiling Set 2 HX1	Array 2 of 10	chr2	65,850,426	181,926,682
C7264-00-01	MM8Tiling Set 2 HX1	Array 2 of 10	chr3	3,000,001	143,307,173
C7265-00-01	MM8Tiling Set 3 HX1	Array 3 of 10	chr3	143,307,273	159,871,956
			chr4	3,006,417	155,029,602
			chr5	3,000,001	92,685,503
C7266-00-01	MM8Tiling Set 4 HX1	Array 4 of 10	chr5	92,685,618	152,002,850
			chr5 random	26	2,921,095
			chr6	3,000,001	149,525,609
			chr7	3,000,201	56,647,386
C7267-00-01	MM8Tiling Set 5 HX1	Array 5 of 10	chr7	54,647,476	145,133,950
			chr7 random	141	243,809
			chr8	3,000,026	132,084,963
			chr8 random	16	206,850
			chr9	3,000,026	40,163,952
C7268-00-01	MM8Tiling Set 6 HX1	Array 6 of 10	chr9	40,164,052	124,000,522
			chr9 random	26	16,954
			chr10	3,000,218	129,957,189
			chr10 random	26	10,495
			chr11	3,000,001	41,900,738
C7269-00-01	MM8Tiling Set 7 HX1	Array 7 of 10	chr11	41,900,844	121,798,365
			chr12	3,000,001	120,463,003
			chr13	3,001,721	55,855,799
C7270-00-01	MM8Tiling Set 8 HX1	Array 8 of 10	chr13	55,855,898	120,614,219
			chr13 random	6	436,079
			chr14	3,001,139	123,976,001
			chr15	3,000,001	76,463,380
C7271-00-01	MM8Tiling Set 9 HX1	Array 9 of 10	chr15	76,463,500	103,492,425
			chr15 random	16	105,806
			chr16	3,000,056	98,252,277
			chr17	3,000,001	95,177,318
			chr17 random	51	88,976
			chr18	3,000,001	40,478,067
C7272-00-01	MM8Tiling Set 10 HX1	Array 10 of 10	chr18	40,478,152	90,736,262
			chr19	3,000,156	61,321,048
			chrM	26	16,224
			chrUn random	126	1,539,898
			chrX	3,000,026	165,555,977
			chrX random	326	39,548
			chrY	6	2,729,267
			chrY random	6,484	14,577,549

Mus musculus - Economy

Source: UCSC Build: MM8 Probe Length: 50-75mer Median Probe Spacing: 203bp Platform: HD2 Probes per Array: 2,100,000 Feature Size: 13μm x 13μm Array Dimensions: 62mm x 14mm Overall Slide Dimensions: 1" x 3" (25 x 75mm) Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number	Design Name	Description	Chromosome	Tiling Start	Tiling Stop
C7278-SET-01	MM8 ECONOMY Tiling Set HX1	4 Array Set	Whole Genome 4-Array Set
C7274-00-01	MM8 ECONOMY Tiling Set 1 HX1	Array 1 of 4	chr1	3,000,159	197,066,856
			chr1 random	104	172,149
			chr2	3,006,248	181,926,726
			chr3	3,000,003	159,872,112
			chr4	3,006,469	119,314,705
C7275-00-01	MM8 ECONOMY Tiling Set 2 HX1	Array 2 of 4	chr4	119,312,724	155,029,701
			chr5	3,004,823	152,002,929
			chr5 random	357	2,921,247
			chr6	3,000,003	149,525,594
			chr7	3,002,500	145,134,020
			chr7 random	830	243,836
			chr8	3,001,012	132,084,168
			ch8 random	335	206,961
			chr9	3,038,422	39,288,818
C7276-00-01	MM8 ECONOMY Tiling Set 3 HX1	Array 3 of 4	chr9	39,287,970	123,999,613
			chr9 random	1	16,784
			chr10	3,002,173	129,952,335
			chr10 random	1	10,556
			chr11	3,005,469	121,798,411
			chr12	3,000,003	120,463,159
			chr13	3,002,645	120,614,378
			chr13 random	513	436,191
			chr14	3,000,285	57,853,012
C7277-00-01	MM8 ECONOMY Tiling Set 4 HX1	Array 4 of 4	chr14	57,850,947	123,975,935
			chr15	3,002,688	103,492,224
			chr15 random	1	105,932
			chr16	3,001,531	98,252,333
			chr17	3,000,003	95,177,217
			chr17 random	61	88,403
			chr18	3,000,971	90,736,071
			chr19	3,000,196	61,321,190
			chrM	1	16,299
			chrUn random	565	1,539,866
			chrX	3,007,929	165,556,094
			chrX random	3,484	39,696
			chrY	151	2,729,286
			chrY random	6,494	14,577,732

Rattus norvegicus

Source: UCSC Build: RN34 Probe Length: 50-75mer Median Probe Spacing: 100bp Platform: HD2 Probes per Array: 2,100,000 Feature Size: 13μm x 13μm Array Dimensions: 62mm x 14mm Overall Slide Dimensions: 1" x 3" (25 x 75mm) Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number	Design Name	Description	Chromosome	Tiling Start	Tiling Stop
C7290-SET-01	RN34Tiling Set HX1	10 Array Set	Whole Genome 10-Array Set
C7279-00-01	RN34Tiling Set 1 HX1	Array 1 of 10	chr1	1	267,910,774
			chr1 random	1	3,884,837
			chr2	26	13,557,674
C7281-00-01	RN34Tiling Set 2 HX1	Array 2 of 10	chr2	13,557,774	258,200,598
			chr2 random	26,460	4,341,770
			chr3	176	34,210,905
C7282-00-01	RN34Tiling Set 3 HX1	Array 3 of 10	chr3	34,211,015	171,063,124
			chr3 random	5,681	1,719,288
			chr4	171	133,406,152
C7283-00-01	RN34Tiling Set 4 HX1	Array 4 of 10	chr4	133,406,273	187,125,435
			chr4 random	341	2,119,523
			Chr5	3,947	173,096,030
			Chr5 random	31	2,145,029
			Chr6	5,546	46,956,292
C7284-00-01	RN34Tiling Set 5 HX1	Array 5 of 10	Chr6	46,956,377	147,630,631
			Chr6 random	26	1,765,697
			Chr7	6,147	143,002,565
			Chr7 random	136	1,172,477
			Chr8	126	29,013,150
C7285-00-01	RN34Tiling Set 6 HX1	Array 6 of 10	Chr8	29,013,250	129,041,601
			Chr8 random	62	886,901
			Chr9	3,248	113,440,328
			Chr9 random	194	1,163,513
			chr10	1	48,202,137
C7286-00-01	RN34Tiling Set 7 HX1	Array 7 of 10	chr10	48,202,262	110,718,677
			chr10 random	2	869,685
			chr11	5,218	87,757,579
			chr11 random	26	1,273,526
			chr12	531	46,782,101
			chr12 random	7,324	947,965
			chr13	16	74,362,754
C7287-00-01	RN34Tiling Set 8 HX1	Array 8 of 10	chr13	74,362,854	111,151,339
			chr13 random	26	608,244
			chr14	1,887	112,193,818
			chr14 random	12	1,824,996
			chr15	666	109,757,551
			chr15 random	2	1,605,910
			chr16	6	14,661,336
C7288-00-01	RN34Tiling Set 9 HX1	Array 9 of 10	chr16	14,661,446	90,232,174
			chr16 random	1	1,399,983
			chr17	7	97,295,476
			chr17 random	3,168	613,253
			chr18	873	87,261,725
			chr18 random	46	594,412
			chr19	21	15,708,114
C7289-00-01	RN34Tiling Set 10 HX1	Array 10 of 10	chr19	15,708,224	59,213,078
			chr19 random	5,698	977,657
			Chr20	26	55,263,625
			Chr20 random	1	592,543
			chrM	26	16,211
			chrX	12	160,699,113
			chrX random	266	1,977,439

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