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ChIP-chip - Whole-Genome Designs


2.1M Whole-Genome Tiling Sets

The higher density of the 2.1M array format means fewer arrays are needed to analyze the whole genome of complex organisms at high resolution. Whole-genome formats provide two options: a 10-array set at 100bp probe interval or a 4-array set at >200bp probe interval. For model organisms, a single 2.1M array slide has enough capacity to tile through the entire genome (55bp probe interval for D. melanogaster and 40bp probe interval for C. elegans).

385K Whole-Genome Tiling Sets

These sets tile uniformly across all unique regions of a genome at an average probe spacing of 100bp or less. Human, mouse, Arabidopsis, rat, dog, chicken and other genomes are currently available. Interrogate the whole genome or ENCODE regions to discover protein/DNA interactions in an unbiased manner.

For all Whole-Genome designs, you have the option of ordering the entire genome set or individual arrays within the set.

Arabidopsis thaliana
NimbleGen 385K Array Format: 385K
Source: NCBI
Build: TAIR6.0
Probe Length: 50mer
Median Probe Spacing: 90bp
Accession Numbers: NC_003070,NC_003071, NC_003074,NC_003075,NC_003076
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 3-Array Set
Delivery Workflow. Click to learn more... 05224209001 A. tha ChIP 385K WG-T Set-3 Arr Del
Service Workflow. Click to learn more... C4348001-SET-01 ATH6 ChIP
See Below
Array 1 of 3
Delivery Workflow. Click to learn more... 05542863001 A. tha ChIP 385K WG-T 1-3 Arr Del
Service Workflow. Click to learn more... C4348001-01-01 ATH6 ChIP 1
chr1 106 30,432,534
chr2 1,001 9,687,876
Array 2 of 3
Delivery Workflow. Click to learn more... 05542871001 A. tha ChIP 385K WG-T 2-3 Arr Del
Service Workflow. Click to learn more... C4348001-02-01 ATH6 ChIP 2
chr2 9,687,916 19,704,755
chr3 1 23,470,742
chr4 1,001 6,133,069
Array 3 of 3
Delivery Workflow. Click to learn more... 05542880001 A. tha ChIP 385K WG-T 3-3 Arr Del
Service Workflow. Click to learn more... C4348001-03-01 ATH6 ChIP 3
chr4 6,133,109 18,584,924
chr5 1 26,992,695
Caenorhabditis elegans
2.1M Caenorhabditis elegans
NimbleGen 2.1M Array Format: 2.1M
Source: UCSC
Build: CE180
Probe Length: 50-75mer
Median Probe Spacing: 40bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Array 1 of 1
Delivery Workflow. Click to learn more... 05542316001 C. ele ChIP 2.1M WG-T Arr Del
Service Workflow. Click to learn more... C6781-00-01 CE180 Tiling Set HX1
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
385K Caenorhabditis elegans
NimbleGen 385K Array Format: 385K
Source: UCSC
Build: CE2
Probe Length: 50mer
Median Probe Spacing: 86bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 3-Array Set
Delivery Workflow. Click to learn more... 05224225001 C. ele ChIP 385K WG-T Set-3 Arr Del
Service Workflow. Click to learn more... C4533-SET-01 C elegans ChIP
See Below
Array 1 of 3
Delivery or Service Workflow. Click to learn more... C4533-01-01 C elegans ChIP01
chrI 1 15,080,469
chrII 1 15,279,267
chrIII 1 3,178,860
Array 2 of 3
Delivery or Service Workflow. Click to learn more... C4533-02-01 C elegans ChIP02
chrIII 3,178,896 13,783,302
chrIV 1 17,493,781
chrM 1 13,738
chrV 1 5,341,967
Array 3 of 3
Delivery or Service Workflow. Click to learn more... C4533-03-01 C elegans ChIP03
chrV 5,342,003 20,922,215
chrX 1 17,718,822
Chicken
NimbleGen 385K Array Format: 385K
Source: UCSC
Build: galGal3
Probe Length: 50mer
Median Probe Spacing: 100bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 27 Array Set
Delivery or Service Workflow. Click to learn more... C4530-SET-01 Gal3Tiling Set
See Below
Array 1 of 27
Delivery or Service Workflow. Click to learn more... C4530-01-01 Gal3Tiling Set 1
chr1 1 39,473,000
Array 2 of 27
Delivery or Service Workflow. Click to learn more... C4530-02-01 Gal3Tiling Set 2
chr1 39,473,050 80,386,539
Array 3 of 27
Delivery or Service Workflow. Click to learn more... C4530-03-01 Gal3Tiling Set 3
chr1 80,386,589 119,731,713
Array 4 of 27
Delivery or Service Workflow. Click to learn more... C4530-04-01 Gal3Tiling Set 4
chr1 119,731,763 159,240,269
Array 5 of 27
Delivery or Service Workflow. Click to learn more... C4530-05-01 Gal3Tiling Set 5
chr1 159,240,319 198,779,897
Array 6 of 27
Delivery or Service Workflow. Click to learn more... C4530-06-01 Gal3Tiling Set 6
chr1 198,779,947 200,993,971
chr1 random 1 222,058
chr2 1 37,050,048
Array 7 of 27
Delivery or Service Workflow. Click to learn more... C4530-07-01 Gal3Tiling Set 7
chr2 37,050,098 77,948,675
Array 8 of 27
Delivery or Service Workflow. Click to learn more... C4530-08-01 Gal3Tiling Set 8
chr2 77,948,725 117,274,559
Array 9 of 27
Delivery or Service Workflow. Click to learn more... C4530-09-01 Gal3Tiling Set 9
chr2 117,274,609 154,873,711
chr2 random 1 142,793
chr3 1 1,760,406
Array 10 of 27
Delivery or Service Workflow. Click to learn more... C4530-10-01 Gal3Tiling Set 10
chr3 1,760,456 42,540,444
Array 11 of 27
Delivery or Service Workflow. Click to learn more... C4530-11-01 Gal3Tiling Set 11
chr3 42,540,494 81,756,614
Array 12 of 27
Delivery or Service Workflow. Click to learn more... C4530-12-01 Gal3Tiling Set 12
chr3 81,756,664 113,657,692
chr4 39 7,608,274
Array 13 of 27
Delivery or Service Workflow. Click to learn more... C4530-13-01 Gal3Tiling Set 13
chr4 7,608,324 48,372,531
Array 14 of 27
Delivery or Service Workflow. Click to learn more... C4530-14-01 Gal3Tiling Set 14
chr4 48,372,581 87,660,311
Array 15 of 27
Delivery or Service Workflow. Click to learn more... C4530-15-01 Gal3Tiling Set 15
chr4 87,660,361 94,230,338
chr4 random 1 180,704
chr5 1 34,275,589
Array 16 of 27
Delivery or Service Workflow. Click to learn more... C4530-16-01 Gal3Tiling Set 16
chr5 34,275,639 62,238,856
chr5 random 1 27,851
chr6 1,500,001 12,842,108
Array 17 of 27
Delivery or Service Workflow. Click to learn more... C4530-17-01 Gal3Tiling Set 17
chr6 12,842,158 37,400,433
chr6 random 1 34,129
chr7 1 16,259,739
Array 18 of 27
Delivery or Service Workflow. Click to learn more... C4530-18-01 Gal3Tiling Set 18
chr7 16,259,789 38,384,711
chr7 random 1 103,968
chr8 1 18,661,092
Array 19 of 27
Delivery or Service Workflow. Click to learn more... C4530-19-01 Gal3Tiling Set 19
chr10 1 4,527,828
chr8 18,661,142 30,671,698
chr8 random 1 420,684
chr9 1,500,001 25,554,304
Array 20 of 27
Delivery or Service Workflow. Click to learn more... C4530-20-01 Gal3Tiling Set 20
chr10 4,527,878 22,556,366
chr10 random 1 13,674
chr11 1 21,928,091
chr11 random 1 72,609
chr12 1 110,850
Array 21 of 27
Delivery or Service Workflow. Click to learn more... C4530-21-01 Gal3Tiling Set 21
chr12 110,900 20,536,630
chr12 random 1 7,004
chr13 500,001 18,911,876
chr13 random 1 35,727
chr14 1 1,168,043
Array 22 of 27
Delivery or Service Workflow. Click to learn more... C4530-22-01 Gal3Tiling Set 22
chr14 1,168,093 15,819,374
chr15 1 12,968,127
chr16 1 432,900
chr16 random 1 246,201
chr17 500,001 11,182,467
chr17 random 1 2,851
chr18 1 910,609
Array 23 of 27
Delivery or Service Workflow. Click to learn more... C4530-23-01 Gal3Tiling Set 23
chr18 910,659 10,925,251
chr18 random 1 11,883
chr19 1 9,939,630
chr20 1 13,986,179
chr20 random 1 75,038
chr21 1 5,982,361
Array 24 of 27
Delivery or Service Workflow. Click to learn more... C4530-24-01 Gal3Tiling Set 24
chr21 5,982,411 6,959,606
chr22 1 3,936,495
chr22 random 1 156,124
chr23 1 6,042,119
chr24 1 6,400,030
chr25 1 2,031,765
chr25 random 1 80,294
chr26 1 5,102,354
chr27 1 4,841,948
chr28 1 4,511,963
chr28 random 1 105,400
chr32 1 951
chrW 1 259,614
chrW random 1 729,474
chrZ 1 7,526,271
Array 25 of 27
Delivery or Service Workflow. Click to learn more... C4530-25-01 Gal3Tiling Set 25
chrZ 7,526,321 50,886,328
Array 26 of 27
Delivery or Service Workflow. Click to learn more... C4530-26-01 Gal3Tiling Set 26
chrE22C19W28 E50C23 1 895,233
chrE22C19W28 E50C23 random 1 191,057
chrE64 1 49,833
chrE64 random 1 557,616
chrUn random 1 17,557,610
chrZ 50,886,378 74,602,257
chrZ random 1 346,154
Array 27 of 27
Delivery or Service Workflow. Click to learn more... C4530-27-01 Gal3Tiling Set 27
chrUn random 17,557,660 63,870,725
Dog
NimbleGen 385K Array Format: 385K
Source: UCSC
Build: canFam2
Probe Length: 50mer
Median Probe Spacing: 100bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 37 Array Set
Delivery or Service Workflow. Click to learn more... C4529-SET-01 canFam2Tiling Set
See Below
Array 1 of 37
Delivery or Service Workflow. Click to learn more... C4529-01-01 canFam2Tiling Set 1
chr1 3,012,394 62,278,628
Array 2 of 37
Delivery or Service Workflow. Click to learn more... C4529-02-01 canFam2Tiling Set 2
chr1 62,278,678 125,616,165
chr2 3,000,001 5,603,265
Array 3 of 37
Delivery or Service Workflow. Click to learn more... C4529-03-01 canFam2Tiling Set 3
chr2 5,603,315 69,134,091
Array 4 of 37
Delivery or Service Workflow. Click to learn more... C4529-04-01 canFam2Tiling Set 4
chr2 69,134,594 88,407,229
chr3 3,000,001 48,179,151
Array 5 of 37
Delivery or Service Workflow. Click to learn more... C4529-05-01 canFam2Tiling Set 5
chr3 48,179,201 94,714,891
chr4 3,010,521 18,819,981
Array 6 of 37
Delivery or Service Workflow. Click to learn more... C4529-06-01 canFam2Tiling Set 6
chr4 18,820,031 81,540,804
Array 7 of 37
Delivery or Service Workflow. Click to learn more... C4529-07-01 canFam2Tiling Set 7
chr4 81,540,854 91,483,852
chr5 3,009,839 55,204,271
Array 8 of 37
Delivery or Service Workflow. Click to learn more... C4529-08-01 canFam2Tiling Set 8
chr5 55,204,321 91,976,388
chr6 3,015,844 27,099,882
Array 9 of 37
Delivery or Service Workflow. Click to learn more... C4529-09-01 canFam2Tiling Set 9
chr6 27,100,060 80,642,094
chr7 3,000,001 12,088,918
Array 10 of 37
Delivery or Service Workflow. Click to learn more... C4529-10-01 canFam2Tiling Set 10
chr7 12,088,968 75,099,510
Array 11 of 37
Delivery or Service Workflow. Click to learn more... C4529-11-01 canFam2Tiling Set 11
chr7 75,099,560 83,999,176
chr8 3,003,063 58,081,791
Array 12 of 37
Delivery or Service Workflow. Click to learn more... C4529-12-01 canFam2Tiling Set 12
chr8 58,081,841 77,307,274
chr9 3,000,001 44,485,970
Array 13 of 37
Delivery or Service Workflow. Click to learn more... C4529-13-01 canFam2Tiling Set 13
chr9 44,486,020 64,413,461
chr10 3,003,191 44,470,365
Array 14 of 37
Delivery or Service Workflow. Click to learn more... C4529-14-01 canFam2Tiling Set 14
chr10 44,470,415 72,488,496
chr11 3,002,836 38,777,021
Array 15 of 37
Delivery or Service Workflow. Click to learn more... C4529-15-01 canFam2Tiling Set 15
chr11 38,777,071 77,416,425
chr12 3,003,326 27,657,072
Array 16 of 37
Delivery or Service Workflow. Click to learn more... C4529-16-01 canFam2Tiling Set 16
chr12 27,657,122 75,515,277
chr13 3,003,109 18,623,175
Array 17 of 37
Delivery or Service Workflow. Click to learn more... C4529-17-01 canFam2Tiling Set 17
chr13 18,623,225 66,182,432
chr14 3,005,181 19,249,997
Array 18 of 37
Delivery or Service Workflow. Click to learn more... C4529-18-01 canFam2Tiling Set 18
chr14 19,250,047 63,938,183
chr15 3,013,266 20,943,569
Array 19 of 37
Delivery or Service Workflow. Click to learn more... C4529-19-01 canFam2Tiling Set 19
chr15 20,943,619 67,211,493
chr16 3,008,838 19,476,430
Array 20 of 37
Delivery or Service Workflow. Click to learn more... C4529-20-01 canFam2Tiling Set 20
chr16 19,476,480 62,570,129
chr17 3,000,001 20,271,895
Array 21 of 37
Delivery or Service Workflow. Click to learn more... C4529-21-01 canFam2Tiling Set 21
chr17 20,271,945 67,340,432
chr18 3,000,001 20,419,229
Array 22 of 37
Delivery or Service Workflow. Click to learn more... C4529-22-01 canFam2Tiling Set 22
chr18 20,419,279 58,870,922
chr19 3,000,001 28,339,210
Array 23 of 37
Delivery or Service Workflow. Click to learn more... C4529-23-01 canFam2Tiling Set 23
chr19 28,339,260 56,771,301
chr20 3,000,001 37,242,822
Array 24 of 37
Delivery or Service Workflow. Click to learn more... C4529-24-01 canFam2Tiling Set 24
chr20 37,242,872 61,280,721
chr21 3,001,882 44,745,333
Array 25 of 37
Delivery or Service Workflow. Click to learn more... C4529-25-01 canFam2Tiling Set 25
chr21 44,745,383 54,024,600
chr22 3,000,919 55,735,714
Array 26 of 37
Delivery or Service Workflow. Click to learn more... C4529-26-01 canFam2Tiling Set 26
chr22 55,735,764 64,394,174
chr23 3,000,001 55,389,494
chr24 3,000,854 5,202,800
Array 27 of 37
Delivery or Service Workflow. Click to learn more... C4529-27-01 canFam2Tiling Set 27
chr24 5,202,850 50,763,049
chr25 3,000,846 21,376,267
Array 28 of 37
Delivery or Service Workflow. Click to learn more... C4529-28-01 canFam2Tiling Set 28
chr25 21,376,317 54,563,572
chr26 3,007,786 33,257,971
Array 29 of 37
Delivery or Service Workflow. Click to learn more... C4529-29-01 canFam2Tiling Set 29
chr26 33,258,021 42,029,628
chr27 3,000,099 48,905,266
chr28 3,003,108 12,569,835
Array 30 of 37
Delivery or Service Workflow. Click to learn more... C4529-30-01 canFam2Tiling Set 30
chr28 12,569,885 44,190,932
chr29 3,023,514 33,081,560
Array 31 of 37
Delivery or Service Workflow. Click to learn more... C4529-31-01 canFam2Tiling Set 31
chr29 33,081,610 44,828,998
chr30 3,000,001 43,205,974
chr31 3,000,365 14,273,595
Array 32 of 37
Delivery or Service Workflow. Click to learn more... C4529-32-01 canFam2Tiling Set 32
chr31 14,273,645 42,262,811
chr32 3,000,482 38,020,796
Array 33 of 37
Delivery or Service Workflow. Click to learn more... C4529-33-01 canFam2Tiling Set 33
chr32 38,020,910 41,730,743
chr33 3,000,001 34,424,222
chr34 3,000,524 29,859,548
Array 34 of 37
Delivery or Service Workflow. Click to learn more... C4529-34-01 canFam2Tiling Set 34
chr34 29,859,598 45,128,234
chr35 3,000,157 29,533,501
chr36 3,001,322 22,745,468
Array 35 of 37
Delivery or Service Workflow. Click to learn more... C4529-35-01 canFam2Tiling Set 35
chr36 22,745,641 33,840,292
chr37 3,004,135 33,915,094
chr38 3,016,144 20,785,825
Array 36 of 37
Delivery or Service Workflow. Click to learn more... C4529-36-01 canFam2Tiling Set 36
chr38 20,785,875 26,897,637
chrX 9 80,254,721
Array 37 of 37
Delivery or Service Workflow. Click to learn more... C4529-37-01 canFam2Tiling Set 37
chrM 1 16,694
chrUn 28,809 86,546,042
chrX 80,254,771 126,883,716
Drosophila melanogaster
2.1M Drosophila melanogaster
NimbleGen 2.1M Array Format: 2.1M
Source: UCSC
Build: DM5
Probe Length: 50-75mer
Median Probe Spacing: 55bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Array 1 of 1
Delivery Workflow. Click to learn more... 05542308001 D. mel ChIP 2.1M WG-T Arr Del
Service Workflow. Click to learn more... C7245-00-01 DM5 Tiling Set HX1
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
385K Drosophila melanogaster
NimbleGen 385K Array Format: 385K
Source: UCSC
Build: DM2
Probe Length: 50mer
Median Probe Spacing: 97bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 3 Array Set
Delivery Workflow. Click to learn more... 05224268001 D. mel ChIP 385K WG-T Set-3 Arr Del
Service Workflow. Click to learn more... C4532-SET-01 DMEL ChIP Set
See Below
Array 1 of 3
Delivery or Service Workflow. Click to learn more... C4532-01-01 DMEL ChIP Set 1
chr2L 155 22,403,093
chr2R 1 18,175,156
Array 2 of 3
Delivery or Service Workflow. Click to learn more... C4532-02-01 DMEL ChIP Set 2
chr2R 18,175,203 20,766,579
chr2h 1,769 1,693,289
chr3L 94 23,764,120
chr3R 1 13,202,299
Array 3 of 3
Delivery or Service Workflow. Click to learn more... C4532-03-01 DMEL ChIP Set 3
chr3R 13,202,346 27,904,842
chr3h 436 2,953,888
chr4 1,724 1,281,635
chr4h 2,261 88,040
chrM 1 14,774
chrU 168,223 8,721,504
chrX 10,779 22,223,781
chrXh 3,311 358,411
chrYh 1,862 394,283
Escherichia coli
NimbleGen 385K Array Format: 385K
Source: RefSeq
Build: NC_000913.1
Probe Length: 50mer
Median Probe Spacing: 24bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Array 1 of 1
Delivery Workflow. Click to learn more... 05542901001 E. col ChIP 385K WG-T Arr Del
Service Workflow. Click to learn more... C4215-00-01 Ecoli K12 ChIP
 
Human
2.1M Human
NimbleGen 2.1M Array Format: 2.1M
Source: UCSC
Build: HG18
Probe Length: 50-75mer
Median Probe Spacing: 100bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 10 Array Set
Delivery Workflow. Click to learn more... 05327768001 Human ChIP 2.1M WG-T Set-10 Arr Del
Service Workflow. Click to learn more... C7257-SET-01 HG18Tiling Set HX1
See Below
Array 1 of 10
Delivery Workflow. Click to learn more... 05542359001 Human ChIP 2.1M WG-T 1-10 Arr Del
Service Workflow. Click to learn more... C7246-00-01 HG18Tiling Set 1 HX1
chr1 505 247,195,005
chr2 321 60,027,826
Array 2 of 10
Delivery Workflow. Click to learn more... 05542367001 Human ChIP 2.1M WG-T 2-10 Arr Del
Service Workflow. Click to learn more... C7247-00-01 HG18Tiling Set 2 HX1
chr2 6,002,792 242,951,119
chr3 35,001 106,782,710
Array 3 of 10
Delivery Workflow. Click to learn more... 05542375001 Human ChIP 2.1M WG-T 3-10 Arr Del
Service Workflow. Click to learn more... C7248-00-01 HG18Tiling Set 3 HX1
chr3 106,782,825 199,501,827
chr4 216 191,273,063
chr5 64,925 2,304,112
Array 4 of 10
Delivery Workflow. Click to learn more... 05542383001 Human ChIP 2.1M WG-T 4-10 Arr Del
Service Workflow. Click to learn more... C7249-00-01 HG18Tiling Set 4 HX1
chr5 2,304,217 180,857,866
chr6 5,001 111,919,925
Array 5 of 10
Delivery Workflow. Click to learn more... 05542391001 Human ChIP 2.1M WG-T 5-10 Arr Del
Service Workflow. Click to learn more... C7250-00-01 HG18Tiling Set 5 HX1
chr6 111,920,005 170,899,992
chr7 49,317 158,821,424
chr8 521 74,730,105
Array 6 of 10
Delivery Workflow. Click to learn more... 05542405001 Human ChIP 2.1M WG-T 6-10 Arr Del
Service Workflow. Click to learn more... C7251-00-01 HG18Tiling Set 6 HX1
chr8 74,730,205 146,274,826
chr9 516 140,273,252
chr10 1,773,517 101,402,412
Array 7 of 10
Delivery Workflow. Click to learn more... 05542413001 Human ChIP 2.1M WG-T 7-10 Arr Del
Service Workflow. Click to learn more... C7253-00-01 HG18Tiling Set 7 HX1
chr10 101,402,517 135,374,737
chr11 62,725 134,452,384
chr12 17,426 121,385,801
Array 8 of 10
Delivery Workflow. Click to learn more... 05542421001 Human ChIP 2.1M WG-T 8-10 Arr Del
Service Workflow. Click to learn more... C7254-00-01 HG18Tiling Set 8 HX1
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
Array 9 of 10
Delivery Workflow. Click to learn more... 05542430001 Human ChIP 2.1M WG-T 9-10 Arr Del
Service Workflow. Click to learn more... C7255-00-01 HG18Tiling Set 9 HX1
chr16 6,248,403 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
Array 10 of 10
Delivery Workflow. Click to learn more... 05542448001 Human ChIP 2.1M WG-T 10-10 Arr Del
Service Workflow. Click to learn more... C7256-00-01 HG18Tiling Set 10 HX1
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
2.1M Human - Economy
NimbleGen 2.1M Array Format: 2.1M
Source: UCSC
Build: HG18
Probe Length: 50-75mer
Median Probe Spacing: 205bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 4 Array Set
Delivery Workflow. Click to learn more... 05327890001 Human ChIP 2.1M Econ WG-T Set-4 Arr Del
Service Workflow. Click to learn more... C7262-SET-01 HG18 ECONOMY Tiling Set HX1
See Below
Array 1 of 4
Delivery Workflow. Click to learn more... 05542456001 Human ChIP 2.1M Econ WG-T 1-4 Arr Del
Service Workflow. Click to learn more... C7258-00-01 HG18 ECONOMY Tiling Set 1 HX1
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
Array 2 of 4
Delivery Workflow. Click to learn more... 05542464001 Human ChIP 2.1M Econ WG-T 2-4 Arr Del
Service Workflow. Click to learn more... C7259-00-01 HG18 ECONOMY Tiling Set 2 HX1
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
Array 3 of 4
Delivery Workflow. Click to learn more... 05542472001 Human ChIP 2.1M Econ WG-T 3-4 Arr Del
Service Workflow. Click to learn more... C7260-00-01 HG18 ECONOMY Tiling Set 3 HX1
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
Array 4 of 4
Delivery Workflow. Click to learn more... 05542499001 Human ChIP 2.1M Econ WG-T 4-4 Arr Del
Service Workflow. Click to learn more... C7261-00-01 HG18 ECONOMY Tiling Set 4 HX1
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
385K Human
NimbleGen 385K Array Format: 385K
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 38 Array Set
Delivery or Service Workflow. Click to learn more... C4524-SET-01 HG18Tiling Set
See Below
Array 1 of 38
Delivery or Service Workflow. Click to learn more... C4524-01-01 HG18Tiling Set 1
chr1 1,644 77,833,868
Array 2 of 38
Delivery or Service Workflow. Click to learn more... C4524-02-01 HG18Tiling Set 2
chr1 77,833,918 175,048,429
Array 3 of 38
Delivery or Service Workflow. Click to learn more... C4524-03-01 HG18Tiling Set 3
chr1 175,050,895 247,197,901
chr1 random 1,609 1,660,118
chr2 2,789 166,769
Array 4 of 38
Delivery or Service Workflow. Click to learn more... C4524-04-01 HG18Tiling Set 4
chr2 166,819 71,983,140
Array 5 of 38
Delivery or Service Workflow. Click to learn more... C4524-05-01 HG18Tiling Set 5
chr2 71,983,425 150,976,181
Array 6 of 38
Delivery or Service Workflow. Click to learn more... C4524-06-01 HG18Tiling Set 6
chr2 150,976,231 221,986,862
Array 7 of 38
Delivery or Service Workflow. Click to learn more... C4524-07-01 HG18Tiling Set 7
chr2 221,986,912 242,751,051
chr2 random 1 185,538
chr3 35,001 53,042,567
Array 8 of 38
Delivery or Service Workflow. Click to learn more... C4524-08-01 HG18Tiling Set 8
chr3 53,043,153 130,523,638
Array 9 of 38
Delivery or Service Workflow. Click to learn more... C4524-09-01 HG18Tiling Set 9
chr3 130,523,688 199,446,729
chr3 random 1,180 749,171
chr4 6,124 5,907,785
Array 10 of 38
Delivery or Service Workflow. Click to learn more... C4524-10-01 HG18Tiling Set 10
chr4 5,907,836 86,895,691
Array 11 of 38
Delivery or Service Workflow. Click to learn more... C4524-11-01 HG18Tiling Set 11
chr4 86,895,741 162,579,935
Array 12 of 38
Delivery or Service Workflow. Click to learn more... C4524-12-01 HG18Tiling Set 12
chr4 162,580,158 191,260,272
chr4 random 1 842,645
chr5 64,882 43,102,632
Array 13 of 38
Delivery or Service Workflow. Click to learn more... C4524-13-01 HG18Tiling Set 13
chr5 43,102,682 120,977,621
Array 14 of 38
Delivery or Service Workflow. Click to learn more... C4524-14-01 HG18Tiling Set 14
chr5 120,977,671 180,836,772
chr5 random 700 141,287
chr6 5,001 14,400,058
Array 15 of 38
Delivery or Service Workflow. Click to learn more... C4524-15-01 HG18Tiling Set 15
chr6 14,400,108 93,424,260
Array 16 of 38
Delivery or Service Workflow. Click to learn more... C4524-16-01 HG18Tiling Set 16
chr6 93,424,310 165,905,673
Array 17 of 38
Delivery or Service Workflow. Click to learn more... C4524-17-01 HG18Tiling Set 17
chr6 165,905,853 170,896,928
chr6 random 723 1,875,488
chr7 34,001 71,893,449
Array 18 of 38
Delivery or Service Workflow. Click to learn more... C4524-18-01 HG18Tiling Set 18
chr7 71,893,499 146,115,149
Array 19 of 38
Delivery or Service Workflow. Click to learn more... C4524-19-01 HG18Tiling Set 19
chr7 146,115,199 158,821,243
chr7 random 66 547,244
chr8 1 64,734,981
Array 20 of 38
Delivery or Service Workflow. Click to learn more... C4524-20-01 HG18Tiling Set 20
chr8 64,735,105 139,834,728
Array 21 of 38
Delivery or Service Workflow. Click to learn more... C4524-21-01 HG18Tiling Set 21
chr8 139,834,778 146,273,006
chr8 random 2,645 943,766
chr9 1,894 87,382,297
Array 22 of 38
Delivery or Service Workflow. Click to learn more... C4524-22-01 HG18Tiling Set 22
chr10 50,001 19,976,990
chr9 87,382,347 140,272,350
chr9 random 1,524 1,146,418
Array 23 of 38
Delivery or Service Workflow. Click to learn more... C4524-23-01 HG18Tiling Set 23
chr10 19,977,040 99,783,066
Array 24 of 38
Delivery or Service Workflow. Click to learn more... C4524-24-01 HG18Tiling Set 24
chr10 99,783,524 135,370,851
chr10 random 899 113,241
chr11 50,001 35,341,402
Array 25 of 38
Delivery or Service Workflow. Click to learn more... C4524-25-01 HG18Tiling Set 25
chr11 35,341,452 117,277,977
Array 26 of 38
Delivery or Service Workflow. Click to learn more... C4524-26-01 HG18Tiling Set 26
chr11 117,278,030 134,450,373
chr11 random 1 215,264
chr12 17,430 58,836,794
Array 27 of 38
Delivery or Service Workflow. Click to learn more... C4524-27-01 HG18Tiling Set 27
chr12 58,836,844 132,289,483
chr13 17,918,001 22,162,992
Array 28 of 38
Delivery or Service Workflow. Click to learn more... C4524-28-01 HG18Tiling Set 28
chr13 22,163,047 95,001,767
Array 29 of 38
Delivery or Service Workflow. Click to learn more... C4524-29-01 HG18Tiling Set 29
chr13 95,001,817 114,127,886
chr13 random 1 186,280
chr14 18,126,852 72,700,758
Array 30 of 38
Delivery or Service Workflow. Click to learn more... C4524-30-01 HG18Tiling Set 30
chr14 72,700,808 106,360,511
chr15 18,303,911 58,530,389
Array 31 of 38
Delivery or Service Workflow. Click to learn more... C4524-31-01 HG18Tiling Set 31
chr15 58,530,439 100,336,874
chr15 random 1 784,326
chr16 1,462 32,788,140
Array 32 of 38
Delivery or Service Workflow. Click to learn more... C4524-32-01 HG18Tiling Set 32
chr16 32,788,379 88,820,540
chr16 random 485 105,474
chr17 1 28,580,036
Array 33 of 38
Delivery or Service Workflow. Click to learn more... C4524-33-01 HG18Tiling Set 33
chr17 28,580,086 78,654,701
chr17 random 1 2,617,362
chr18 1,146 22,939,995
Array 34 of 38
Delivery or Service Workflow. Click to learn more... C4524-34-01 HG18Tiling Set 34
chr18 22,940,045 76,116,085
chr18 random 1 4,250
chr19 11,001 19,529,590
Array 35 of 38
Delivery or Service Workflow. Click to learn more... C4524-35-01 HG18Tiling Set 35
chr19 19,529,928 63,805,962
chr19 random 8,246 301,805
chr20 11,165 50,138,814
Array 36 of 38
Delivery or Service Workflow. Click to learn more... C4524-36-01 HG18Tiling Set 36
chr20 50,138,864 62,432,160
chr21 9,882,592 46,941,530
chr21 random 1,024 1,679,609
chr22 14,430,066 39,529,828
Array 37 of 38
Delivery or Service Workflow. Click to learn more... C4524-37-01 HG18Tiling Set 37
chr22 39,529,878 49,590,841
chr22 random 1 257,295
chrX 447 85,044,437
Array 38 of 38
Delivery or Service Workflow. Click to learn more... C4524-38-01 HG18Tiling Set 38
chrM 1 16,477
chrX 85,044,487 154,911,115
chrX random 1 1,718,128
chrY 447 57,770,315
Mouse
2.1M Mouse
NimbleGen 2.1M Array Format: 2.1M
Source: UCSC
Build: MM8
Probe Length: 50-75mer
Median Probe Spacing: 100bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 10 Array Set
Delivery Workflow. Click to learn more... 05327903001 Human ChIP 2.1M WG-T Set-10 Arr Del
Service Workflow. Click to learn more... C7273-SET-01 MM8Tiling Set HX1
See Below
Array 1 of 10
Delivery Workflow. Click to learn more... 05542502001 Mouse ChIP 2.1M WG-T 1-10 Arr Del
Service Workflow. Click to learn more... C7264-00-01 MM8Tiling Set 1 HX1
chr1 3,000,001 197,069,505
chr1 random 122 172,060
chr2 3,006,249 65,850,316
Array 2 of 10
Delivery Workflow. Click to learn more... 05542529001 Mouse ChIP 2.1M WG-T 2-10 Arr Del
Service Workflow. Click to learn more... C7265-00-01 MM8Tiling Set 2 HX1
chr2 65,850,426 181,926,682
chr3 3,000,001 143,307,173
Array 3 of 10
Delivery Workflow. Click to learn more... 05542537001 Mouse ChIP 2.1M WG-T 3-10 Arr Del
Service Workflow. Click to learn more... C7266-00-01 MM8Tiling Set 3 HX1
chr3 143,307,273 159,871,956
chr4 3,006,417 155,029,602
chr5 3,000,001 92,685,503
Array 4 of 10
Delivery Workflow. Click to learn more... 05542545001 Mouse ChIP 2.1M WG-T 4-10 Arr Del
Service Workflow. Click to learn more... C7266-00-01 MM8Tiling Set 4 HX1
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
Array 5 of 10
Delivery Workflow. Click to learn more... 05542553001 Mouse ChIP 2.1M WG-T 5-10 Arr Del
Service Workflow. Click to learn more... C7267-00-01 MM8Tiling Set 5 HX1
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
Array 6 of 10
Delivery Workflow. Click to learn more... 05542561001 Mouse ChIP 2.1M WG-T 6-10 Arr Del
Service Workflow. Click to learn more... C7268-00-01 MM8Tiling Set 6 HX1
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
Array 7 of 10
Delivery Workflow. Click to learn more... 05542570001 Mouse ChIP 2.1M WG-T 7-10 Arr Del
Service Workflow. Click to learn more... C7269-00-01 MM8Tiling Set 7 HX1
chr11 41,900,844 121,798,365
chr12 3,000,001 120,463,003
chr13 3,001,721 55,855,799
Array 8 of 10
Delivery Workflow. Click to learn more... 05542588001 Mouse ChIP 2.1M WG-T 8-10 Arr Del
Service Workflow. Click to learn more... C7270-00-01 MM8Tiling Set 8 HX1
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
Array 9 of 10
Delivery Workflow. Click to learn more... 05542596001 Mouse ChIP 2.1M WG-T 9-10 Arr Del
Service Workflow. Click to learn more... C7271-00-01 MM8Tiling Set 9 HX1
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
Array 10 of 10
Delivery Workflow. Click to learn more... 05542600001 Mouse ChIP 2.1M WG-T 10-10 Arr Del
Service Workflow. Click to learn more... C7272-00-01 MM8Tiling Set 10 HX1
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
2.1M Mouse - Economy
NimbleGen 2.1M Array Format: 2.1M
Source: UCSC
Build: MM8
Probe Length: 50-75mer
Median Probe Spacing: 203bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 4 Array Set
Delivery Workflow. Click to learn more... 05327911001 Mouse ChIP 2.1M Econ WG-T Set-4 Arr Del
Service Workflow. Click to learn more... C7278-SET-01 MM8 ECONOMY Tiling Set HX1
See Below
Array 1 of 4
Delivery Workflow. Click to learn more... 05542618001 Mouse ChIP 2.1M Econ WG-T 1-4 Arr Del
Service Workflow. Click to learn more... C7274-00-01 MM8 ECONOMY Tiling Set 1 HX1
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
Array 2 of 4
Delivery Workflow. Click to learn more... 05542626001 Mouse ChIP 2.1M Econ WG-T 2-4 Arr Del
Service Workflow. Click to learn more... C7275-00-01 MM8 ECONOMY Tiling Set 2 HX1
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
Array 3 of 4
Delivery Workflow. Click to learn more... 05542634001 Mouse ChIP 2.1M Econ WG-T 3-4 Arr Del
Service Workflow. Click to learn more... C7276-00-01 MM8 ECONOMY Tiling Set 3 HX1
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
Array 4 of 4
Delivery Workflow. Click to learn more... 05542642001 Mouse ChIP 2.1M Econ WG-T 4-4 Arr Del
Service Workflow. Click to learn more... C7277-00-01 MM8 ECONOMY Tiling Set 4 HX1
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
385K Mouse
NimbleGen 385K Array Format: 385K
Source: UCSC
Build: MM8
Probe Length: 50mer
Median Probe Spacing: 100bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 38-Array Set
Delivery or Service Workflow. Click to learn more... C4527-SET-01 MM8Tiling Set
See Below
Array 1 of 38
Delivery or Service Workflow. Click to learn more... C4527-01-01 MM8Tiling Set 1
chr1 3,000,157 73,220,987
Array 2 of 38
Delivery or Service Workflow. Click to learn more... C4527-02-01 MM8Tiling Set 2
chr1 73,221,037 145,835,677
Array 3 of 38
Delivery or Service Workflow. Click to learn more... C4527-03-01 MM8Tiling Set 3
chr1 145,835,727 197,066,777
chr1 random 102 172,125
chr2 3,006,246 14,803,550
Array 4 of 38
Delivery or Service Workflow. Click to learn more... C4527-04-01 MM8Tiling Set 4
chr2 14,803,600 78,803,469
Array 5 of 38
Delivery or Service Workflow. Click to learn more... C4527-05-01 MM8Tiling Set 5
chr2 78,803,519 144,694,967
Array 6 of 38
Delivery or Service Workflow. Click to learn more... C4527-06-01 MM8Tiling Set 6
chr2 144,695,017 181,926,733
chr3 3,000,001 35,945,810
Array 7 of 38
Delivery or Service Workflow. Click to learn more... C4527-07-01 MM8Tiling Set 7
chr3 35,946,023 105,538,217
Array 8 of 38
Delivery or Service Workflow. Click to learn more... C4527-08-01 MM8Tiling Set 8
chr3 105,538,373 159,872,029
chr4 3,006,467 13,466,829
Array 9 of 38
Delivery or Service Workflow. Click to learn more... C4527-09-01 MM8Tiling Set 9
chr4 13,466,879 86,052,953
Array 10 of 38
Delivery or Service Workflow. Click to learn more... C4527-10-01 MM8Tiling Set 10
chr4 86,053,003 151,907,497
Array 11 of 38
Delivery or Service Workflow. Click to learn more... C4527-11-01 MM8Tiling Set 11
chr4 151,907,547 155,029,701
chr5 3,002,590 66,825,929
Array 12 of 38
Delivery or Service Workflow. Click to learn more... C4527-12-01 MM8Tiling Set 12
chr5 66,825,979 132,198,192
Array 13 of 38
Delivery or Service Workflow. Click to learn more... C4527-13-01 MM8Tiling Set 13
chr5 132,198,242 152,002,824
chr5 random 1 2,921,181
chr6 3,000,336 49,711,116
Array 14 of 38
Delivery or Service Workflow. Click to learn more... C4527-14-01 MM8Tiling Set 14
chr6 49,711,166 116,290,338
Array 15 of 38
Delivery or Service Workflow. Click to learn more... C4527-15-01 MM8Tiling Set 15
chr6 116,290,495 149,525,670
chr7 3,002,498 47,370,177
Array 16 of 38
Delivery or Service Workflow. Click to learn more... C4527-16-01 MM8Tiling Set 16
chr7 47,370,227 115,300,979
Array 17 of 38
Delivery or Service Workflow. Click to learn more... C4527-17-01 MM8Tiling Set 17
chr7 115,301,029 145,133,805
chr7 random 152 243,780
chr8 3,000,187 37,161,130
Array 18 of 38
Delivery or Service Workflow. Click to learn more... C4527-18-01 MM8Tiling Set 18
chr8 37,161,180 106,292,103
Array 19 of 38
Delivery or Service Workflow. Click to learn more... C4527-19-01 MM8Tiling Set 19
chr8 106,292,153 132,084,079
chr8 random 1 206,881
chr9 3,038,420 43,286,226
Array 20 of 38
Delivery or Service Workflow. Click to learn more... C4527-20-01 MM8Tiling Set 20
chr9 43,286,276 105,899,668
Array 21 of 38
Delivery or Service Workflow. Click to learn more... C4527-21-01 MM8Tiling Set 21
chr10 3,002,171 52,787,705
chr9 105,899,718 123,997,618
chr9 random 1 16,735
Array 22 of 38
Delivery or Service Workflow. Click to learn more... C4527-22-01 MM8Tiling Set 22
chr10 52,787,755 117,084,713
Array 23 of 38
Delivery or Service Workflow. Click to learn more... C4527-23-01 MM8Tiling Set 23
chr10 117,084,763 129,952,011
chr10 random 1 10,464
chr11 3,005,467 56,613,072
Array 24 of 38
Delivery or Service Workflow. Click to learn more... C4527-24-01 MM8Tiling Set 24
chr11 56,613,122 117,015,745
Array 25 of 38
Delivery or Service Workflow. Click to learn more... C4527-25-01 MM8Tiling Set 25
chr11 117,015,795 121,798,318
chr12 3,000,001 66,136,890
Array 26 of 38
Delivery or Service Workflow. Click to learn more... C4527-26-01 MM8Tiling Set 26
chr12 66,136,940 120,463,116
chr13 3,001,731 13,478,312
Array 27 of 38
Delivery or Service Workflow. Click to learn more... C4527-27-01 MM8Tiling Set 27
chr13 13,478,362 79,149,705
Array 28 of 38
Delivery or Service Workflow. Click to learn more... C4527-28-01 MM8Tiling Set 28
chr13 79,149,801 120,614,368
chr13 random 1 436,142
chr14 3,000,283 28,012,624
Array 29 of 38
Delivery or Service Workflow. Click to learn more... C4527-29-01 MM8Tiling Set 29
chr14 28,012,674 95,499,352
Array 30 of 38
Delivery or Service Workflow. Click to learn more... C4527-30-01 MM8Tiling Set 30
chr14 95,499,402 123,975,857
chr15 3,001,925 42,329,373
Array 31 of 38
Delivery or Service Workflow. Click to learn more... C4527-31-01 MM8Tiling Set 31
chr15 42,329,489 103,492,126
chr15 random 1 105,912
chr16 3,001,091 5,125,906
Array 32 of 38
Delivery or Service Workflow. Click to learn more... C4527-32-01 MM8Tiling Set 32
chr16 5,126,120 71,871,524
Array 33 of 38
Delivery or Service Workflow. Click to learn more... C4527-33-01 MM8Tiling Set 33
chr16 71,871,574 98,252,249
chr17 3,000,366 42,700,654
Array 34 of 38
Delivery or Service Workflow. Click to learn more... C4527-34-01 MM8Tiling Set 34
chr17 42,700,704 95,177,193
chr17 random 59 88,343
chr18 3,000,001 18,021,916
Array 35 of 38
Delivery or Service Workflow. Click to learn more... C4527-35-01 MM8Tiling Set 35
chr18 18,021,966 81,920,670
Array 36 of 38
Delivery or Service Workflow. Click to learn more... C4527-36-01 MM8Tiling Set 36
chr18 81,920,720 90,736,043
chr19 3,000,194 58,910,586
Array 37 of 38
Delivery or Service Workflow. Click to learn more... C4527-37-01 MM8Tiling Set 37
chr19 58,910,636 61,321,095
chrX 3,007,927 93,883,916
Array 38 of 38
Delivery or Service Workflow. Click to learn more... C4527-38-01 MM8Tiling Set 38
chrM 1 16,293
chrUn random 719 1,539,820
chrX 93,883,966 165,556,020
chrX random 342 39,608
chrY 1 2,728,984
chrY random 6,952 14,577,665
Rat
2.1M Rat
NimbleGen 2.1M Array Format: 2.1M
Source: UCSC
Build: RN34
Probe Length: 50-75mer
Median Probe Spacing: 100bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 10 Array Set
Delivery Workflow. Click to learn more... 05327920001 Rat ChIP 2.1M WG-T Set-10 Arr Del
Service Workflow. Click to learn more... C7290-SET-01 RN34Tiling Set HX1
See Below
Array 1 of 10
Delivery Workflow. Click to learn more... 05542669001 Rat ChIP 2.1M WG-T 1-10 Arr Del
Service Workflow. Click to learn more... C7279-00-01 RN34Tiling Set 1 HX1
chr1 1 267,910,774
chr1 random 1 3,884,837
chr2 26 13,557,674
Array 2 of 10
Delivery Workflow. Click to learn more... 05542677001 Rat ChIP 2.1M WG-T 2-10 Arr Del
Service Workflow. Click to learn more... C7281-00-01 RN34Tiling Set 2 HX1
chr2 13,557,774 258,200,598
chr2 random 26,460 4,341,770
chr3 176 34,210,905
Array 3 of 10
Delivery Workflow. Click to learn more... 05542685001 Rat ChIP 2.1M WG-T 3-10 Arr Del
Service Workflow. Click to learn more... C7282-00-01 RN34Tiling Set 3 HX1
chr3 34,211,015 171,063,124
chr3 random 5,681 1,719,288
chr4 171 133,406,152
Array 4 of 10
Delivery Workflow. Click to learn more... 05542693001 Rat ChIP 2.1M WG-T 4-10 Arr Del
Service Workflow. Click to learn more... C7283-00-01 RN34Tiling Set 4 HX1
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
Array 5 of 10
Delivery Workflow. Click to learn more... 05542707001 Rat ChIP 2.1M WG-T 5-10 Arr Del
Service Workflow. Click to learn more... C7284-00-01 RN34Tiling Set 5 HX1
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
Array 6 of 10
Delivery Workflow. Click to learn more... 05542715001 Rat ChIP 2.1M WG-T 6-10 Arr Del
Service Workflow. Click to learn more... C7285-00-01 RN34Tiling Set 6 HX1
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
Array 7 of 10
Delivery Workflow. Click to learn more... 05542723001 Rat ChIP 2.1M WG-T 7-10 Arr Del
Service Workflow. Click to learn more... C7286-00-01 RN34Tiling Set 7 HX1
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
Array 8 of 10
Delivery Workflow. Click to learn more... 05542731001 Rat ChIP 2.1M WG-T 8-10 Arr Del
Service Workflow. Click to learn more... C7287-00-01 RN34Tiling Set 8 HX1
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
Array 9 of 10
Delivery Workflow. Click to learn more... 05542740001 Rat ChIP 2.1M WG-T 9-10 Arr Del
Service Workflow. Click to learn more... C7288-00-01 RN34Tiling Set 9 HX1
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
Array 10 of 10
Delivery Workflow. Click to learn more... 05542758001 Rat ChIP 2.1M WG-T 10-10 Arr Del
Service Workflow. Click to learn more... C7289-00-01 RN34Tiling Set 10 HX1
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
385K Rat
NimbleGen 385K Array Format: 385K
Source: UCSC
Build: RN3
Probe Length: 50mer
Median Probe Spacing: 100bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Whole Genome 37 Array Set
Delivery or Service Workflow. Click to learn more... C4528-SET-01 RN3Tiling Set
See Below
Array 1 of 37
Delivery or Service Workflow. Click to learn more... C4528-01-01 RN3Tiling Set 1
chr1 5,520 79,919,584
Array 2 of 37
Delivery or Service Workflow. Click to learn more... C4528-02-01 RN3Tiling Set 2
chr1 79,919,634 154,041,905
Array 3 of 37
Delivery or Service Workflow. Click to learn more... C4528-03-01 RN3Tiling Set 3
chr1 154,041,955 224,172,034
Array 4 of 37
Delivery or Service Workflow. Click to learn more... C4528-04-01 RN3Tiling Set 4
chr1 224,172,084 267,910,880
chr2 1 31,354,399
Array 5 of 37
Delivery or Service Workflow. Click to learn more... C4528-05-01 RN3Tiling Set 5
chr2 31,354,517 109,576,919
Array 6 of 37
Delivery or Service Workflow. Click to learn more... C4528-06-01 RN3Tiling Set 6
chr2 109,576,969 185,872,738
Array 7 of 37
Delivery or Service Workflow. Click to learn more... C4528-07-01 RN3Tiling Set 7
chr2 185,872,788 256,774,166
Array 8 of 37
Delivery or Service Workflow. Click to learn more... C4528-08-01 RN3Tiling Set 8
chr2 256,774,216 258,200,683
chr3 1 68,062,290
Array 9 of 37
Delivery or Service Workflow. Click to learn more... C4528-09-01 RN3Tiling Set 9
chr3 68,062,340 139,490,656
Array 10 of 37
Delivery or Service Workflow. Click to learn more... C4528-10-01 RN3Tiling Set 10
chr3 139,490,706 171,063,075
chr4 3,118 39,789,881
Array 11 of 37
Delivery or Service Workflow. Click to learn more... C4528-11-01 RN3Tiling Set 11
chr4 39,789,931 115,751,389
Array 12 of 37
Delivery or Service Workflow. Click to learn more... C4528-12-01 RN3Tiling Set 12
chr4 115,751,720 184,999,983
Array 13 of 37
Delivery or Service Workflow. Click to learn more... C4528-13-01 RN3Tiling Set 13
chr4 185,000,037 187,125,250
chr5 5,760 77,486,463
Array 14 of 37
Delivery or Service Workflow. Click to learn more... C4528-14-01 RN3Tiling Set 14
chr5 77,486,513 151,080,950
Array 15 of 37
Delivery or Service Workflow. Click to learn more... C4528-15-01 RN3Tiling Set 15
chr5 151,081,000 173,096,189
chr6 5,572 47,549,369
Array 16 of 37
Delivery or Service Workflow. Click to learn more... C4528-16-01 RN3Tiling Set 16
chr6 47,549,419 121,154,039
Array 17 of 37
Delivery or Service Workflow. Click to learn more... C4528-17-01 RN3Tiling Set 17
chr6 121,154,089 147,630,634
chr7 6,203 47,765,412
Array 18 of 37
Delivery or Service Workflow. Click to learn more... C4528-18-01 RN3Tiling Set 18
chr7 47,765,462 117,227,981
Array 19 of 37
Delivery or Service Workflow. Click to learn more... C4528-19-01 RN3Tiling Set 19
chr7 117,228,031 143,002,625
chr8 3,406 46,729,790
Array 20 of 37
Delivery or Service Workflow. Click to learn more... C4528-20-01 RN3Tiling Set 20
chr8 46,729,840 113,494,580
Array 21 of 37
Delivery or Service Workflow. Click to learn more... C4528-21-01 RN3Tiling Set 21
chr8 113,494,630 129,041,631
chr9 2,845 56,983,099
Array 22 of 37
Delivery or Service Workflow. Click to learn more... C4528-22-01 RN3Tiling Set 22
chr10 1 10,356,380
chr9 56,983,149 113,440,438
Array 23 of 37
Delivery or Service Workflow. Click to learn more... C4528-23-01 RN3Tiling Set 23
chr10 10,361,275 76,932,657
Array 24 of 37
Delivery or Service Workflow. Click to learn more... C4528-24-01 RN3Tiling Set 24
chr10 76,932,707 110,718,830
chr11 5,213 34,964,213
Array 25 of 37
Delivery or Service Workflow. Click to learn more... C4528-25-01 RN3Tiling Set 25
chr11 34,964,263 87,757,544
chr12 1 19,861,316
Array 26 of 37
Delivery or Service Workflow. Click to learn more... C4528-26-01 RN3Tiling Set 26
chr12 19,861,366 46,782,087
chr13 1 53,625,008
Array 27 of 37
Delivery or Service Workflow. Click to learn more... C4528-27-01 RN3Tiling Set 27
chr13 53,625,058 111,151,398
chr14 1,899 12,118,032
Array 28 of 37
Delivery or Service Workflow. Click to learn more... C4528-28-01 RN3Tiling Set 28
chr14 12,118,082 85,664,357
Array 29 of 37
Delivery or Service Workflow. Click to learn more... C4528-29-01 RN3Tiling Set 29
chr14 85,664,970 112,194,154
chr15 1,104 46,654,817
Array 30 of 37
Delivery or Service Workflow. Click to learn more... C4528-30-01 RN3Tiling Set 30
chr15 46,655,396 109,756,002
chr16 1 8,863,419
Array 31 of 37
Delivery or Service Workflow. Click to learn more... C4528-31-01 RN3Tiling Set 31
chr16 8,863,469 82,449,341
Array 32 of 37
Delivery or Service Workflow. Click to learn more... C4528-32-01 RN3Tiling Set 32
chr16 82,449,391 90,228,347
chr17 137 63,195,861
Array 33 of 37
Delivery or Service Workflow. Click to learn more... C4528-33-01 RN3Tiling Set 33
chr17 63,195,911 97,296,037
chr18 8,835 39,586,512
Array 34 of 37
Delivery or Service Workflow. Click to learn more... C4528-34-01 RN3Tiling Set 34
chr18 39,586,562 87,261,790
chr19 1 21,122,883
Array 35 of 37
Delivery or Service Workflow. Click to learn more... C4528-35-01 RN3Tiling Set 35
chr19 21,122,933 59,213,157
chr20 1 30,044,447
Array 36 of 37
Delivery or Service Workflow. Click to learn more... C4528-36-01 RN3Tiling Set 36
chr20 30,044,497 55,268,200
chrX 1 63,265,501
Array 37 of 37
Delivery or Service Workflow. Click to learn more... C4528-37-01 RN3Tiling Set 37
chrM 1 16,271
chrX 63,265,711 160,698,566
Saccharomyces cerevisiae
NimbleGen 385K Array Format: 385K
Source: UCSC
Build: sacCer1
Probe Length: 50mer
Median Probe Spacing: 32bp
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Chromo-
some
Tiling Start Tiling Stop
Array 1 of 1
Delivery Workflow. Click to learn more... 05542898001 S. cer ChIP 385K WG-T Arr Del
Service Workflow. Click to learn more... C4214-00-01 Scerevisiae ChIP
 
Literature

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

FAQ
Experimental Design
Do you have a recommended protocol for front-end sample processing for producing ChIP DNA? Yes, the protocol that we currently provide is based off a protocol from the Ren laboratory at UCSD. Customers are free to use whichever protocol they would like, but we highly recommend this protocol due to its reproducibility with ChIP-chip arrays. Contact Roche NimbleGen Technical Support if you would like the link to this protocol.
Does Roche NimbleGen perform front-end sample processing (e.g. IP and amplification)? No, Roche NimbleGen is not currently set up to perform contract ChIP-chip experiments for our customers.
What is the minimum number of cells required to perform a Roche NimbleGen recommended ChIP-chip experiment? The minimum number of cells used for a successful ChIP-chip experiment is approximately 1 x 107. However, ChIP reactions in which abundant molecules are being immunoprecipitated (e.g. histones and RNA polymerase II) require a lesser number of cells for a successful experiment. Remember, if you are starting with less material you would need to adjust all of the volumes and concentrations in each protocol.
What is a suitable negative control for ChIP-chip experiments? Many of our customers do not use a negative control (e.g. nonspecific IgG antibody), but it is recommended if this is your first experiment with NimbleGen ChIP-chip. You will want to have your negative control (IgG) co-hybridized with total DNA (input) in order to avoid a high signal/noise ratio that is often seen when the IgG sample is co-hybridized with the immunoprecipitated sample.
What other types of controls are used in a ChIP-chip experiment? The most common experimental control used when performing ChIP is an isotope control, such as nonspecific IgG or antibodies against GST or GFP. A potential pitfall in using these controls is that since the antibodies do not immunoprecipitate the nonspecific DNA yield is often very low. The resulting hybridization also tends to be much noisier and can result in many false positives due to amplification of trace amount of nonspecific DNA. Another, yet rare, control that is sometimes performed is a ChIP using uncrosslinked chromatin. However, many researchers prefer to perform ChIP with an antibody against the protein of interest in a cell line where the protein has been depleted (by target genetic deletion or siRNA). Alternatively, a cell line that does not express the protein of interest could be used as a negative control.
Is it possible to use more than one antibody when performing ChIP or do you recommend using only one antibody per procedure? Yes, many researchers combine multiple antibodies in their ChIP reaction to screen for antibodies that work well. If positive results are observed from this combined antibody approach, one can go back and perform ChIP using individual antibodies against the protein of interest. You can also perform experiments to examine the binding sites for a multi-protein complex by using a pooled sample of antibodies against all subunits of the complex.
What types of beads should I use to capture the immunoprecipitated DNA? There are two competing platforms for ChIP based on what type of beads one uses for immunoprecipitation: agarose protein-A/protein-G beads or magnetic latex immunoglobulin beads. Due to the inherent porosity of the agarose beads, a significant amount of nonspecific DNA binding is observed and consequently a much higher ChIP DNA yield than with magnetic latex beads. Some researchers have claimed that they observe good ChIP results without amplification using agarose beads. However, we recommend magnetic beads because we believe these beads will give much cleaner results.
What should I use as a reference sample? The majority of our customers use total (input) sample as a reference. Using a nonspecific IgG sample is not a suitable reference.
Array Design
Are the probes designed from both strands? No, Roche NimbleGen only designs probes based off of the forward strand.
How does Roche NimbleGen address repetitive elements in the genome for ChIP-chip designs? When available, we utilize conventional repeat masking, as done by the RepeatMasker program http://www.repeatmasker.org/). However, NimbleGen has no access to the repeat libraries necessary to perform this application, so we rely on third parties to supply this type of masked sequence. However, we find that RepeatMasker is often overly aggressive and can mask 50%-55% of human DNA sequence. We have developed our own method of repeat masking which is dependent on the mean frequency of the 15mers which make up each 50mer oligo. A table is made of the count of all 15mers that appear in the genome, from both strands. Then a 15mer window is slid along each oligo, looking up the count of each 15mer in the table, and calculating the average count. A threshold is set, usually 100 for large eukaryotic genomes, and any probe that exceeds that threshold is eliminated from further consideration. Depending on the region of the genome being evaluated, approximately 20-25% of the DNA is excluded. A similar technique is used by other groups. See the following paper for reference: Bioinformatics. 2006 Jan 15;22(2):134-41. WindowMasker: window-based masker for sequenced genomes; Morgulis A, Gertz EM, Schaffer AA, Agarwala R; National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services Building 38A, Room 1003N, 8600 Rockville Pike, Bethesda, MD 20894, USA.
Why do you use 100bp spacing in ChIP-chip designs? Our research/development staff has performed experiments in which human probe spacing is varied; they observe a much poorer signal/noise ratio as well as a dramatic increase in the number of false positives when spacing is greater than 100-120 bp.
What spacing do you recommend for ChIP-chip designs? We recommend probe spacing of 100bp or less.
What are the human ENCODE biologically significant regions that are tiled on 4x72K and human 2.1M Deluxe Promoter arrays? These regions were picked manually by the ENCODE consortium and are deemed biologically significant in terms of transcriptional regulation. The regions include the HOXA cluster (chromosome 7), ß-globin cluster (chromosome 11), and others.
Sample Processing
How much IP sample should be expected prior to the amplification step? The amount of IP sample obtained truly depends on the antibody quality and amount of starting material. A standard ChIP reaction yields DNA fragments in the range of ~100ng.
Do I need to amplify my ChIP samples? Whole genome amplification (WGA) or ligation mediated-PCR (LM-PCR) needs to performed when there is less than 4µg ChIP DNA. NimbleGen recommends the GenomePlex WGA Kits from Sigma-Aldrich.
What method should I use to amplify my ChIP samples? Past and present NimbleGen ChIP-chip customers have had very good experiences working with the Sigma-Aldrich GenomePlex WGA2 Kit (#WGA2-50RXN). The WGA method seems to be easier and the quality of the amplified DNA is quite good. Many customers find that it is difficult to get LM-PCR to work well. For those that are just beginning ChIP-chip studies, we recommend the use of WGA.
What yield should I expect from LM-PCR? A standard ChIP reaction yields less than 100ng DNA. After one round of LM-PCR amplification that yield can increase to a few micrograms. If more DNA is needed, a second round of amplification can be performed.
Does LM-PCR cause bias in the sample? We have found that there tends to be more bias with samples amplified by LM-PCR compared to WGA. We recommend running the amplified DNA on an agarose gel to check for the presence of multiple DNA bands, which indicate poor sample quality. Generally, DNA amplified by WGA gives a smear rather than multiple bands.
Can I use T7 amplification for generating ChIP DNA? Yes, but we have found that customers need to adequately remove all RNA and protein from the sample. T7 amplified samples frequently arrive at Roche NimbleGen with RNA and protein contamination, which results in low labeling yields and subsequently less than adequate amounts of labeled sample to perform an array hybridization.
Why does NimbleGen use 7mer primers for short fragment labeling? We use 7mer primers because they seem to be much more efficient at labeling short DNA fragments (<200 bp). We consistently have trouble obtaining adequate yields for short DNA fragments when using 9mer primers.
What is the difference between 7mer and 9mer labeling for the same samples if it is above 200bp? We are still unclear on the differences between 7mer and 9mer sample labeling for larger DNA fragments. We are in the process of running experiments to test for any differences. Preliminary data has shown that the differences are quite small.
Will all ChIP DNA eventually be labeled using 7mer primers? Labeling ChIP DNA using exclusively 7mer random primers is a possibility. We are in the process of validating 7mer labeling for ChIP-chip. As of now, all ChIP samples should still be labeled using 9mers.
What is the expected yield from labeling reactions? One microgram each of IP and total sample are labeled with Cy5 or Cy3, respectively, using a 9mer primer. Our labeling procedure yields 28µg +/- 10µg for ChIP-chip samples. Samples <200bp yield an average of 10µg per labeling reaction.
Which dye should I use for my experimental and reference sample? We normally label the total sample (input) with Cy3 and the IP sample with Cy5. In the case that you would want to perform a dye swap experiment, you would label total sample (input) with Cy5 and the IP sample with Cy3.
Do I need to order another chip if I am going to perform dye swaps or co-hybridize DNA immunoprecipitated using a nonspecific antibody control? Yes, to perform a dye swap or co-hybridize DNA immunoprecipitated using a nonspecific antibody control you would need to order additional chips.
Sample Requirements for Service
What are the sample requirements for ChIP-chip? For a 385K or 4x72K ChIP-chip array, 3.5µg of ChIP DNA is required per array and for a 2.1M ChIP-chip array, 6.5µg of ChIP DNA is required. In both cases, the concentration of the ChIP DNA should be between 250-1000ng/µl, and the majority of the fragments should greater than 200bp long. The A260/A280 ratios should be at least 1.7 and the A260/A230 ratios should be at least 1.6.
What is the normal ChIP-chip fragment size? What if my fragments are smaller? DNA shearing from a typical ChIP experiment yields 200-1000bp fragments. If the majority of DNA fragments are below 200bp, Roche NimbleGen will have difficulty obtaining adequate labeling yields and hence may not have sufficient material to hybridize to the arrays. However, if your fragments are between 100-1000bp, with the majority of fragments >200bp, than your samples should work well.
How much ChIP DNA do I need to supply if I order the 10 array set? The 10 array set requires approximately 65µg DNA. For a more economical choice for analyzing whole genome protein/DNA interactions, you can use the 4 array set (human and mouse), which requires at least 26µg DNA.
What if my sample concentration or yield is less then required? If your sample does not meet our QC requirements you will be contacted by Roche NimbleGen for replacement samples. If you are unable to supply replacements you still have the option of proceeding with the experiment; however, there may be extra charges attached to this sample and the success of your experiment will not be guaranteed.
Data Analysis
Does Roche NimbleGen normalize ChIP-chip data? No, there is no normalization of ChIP-chip data. However, we do scale the GFF files by subtracting the bi-weight mean for the log-ratio values from each log-ratio value.
Does Roche NimbleGen scale ChIP-chip data? Yes, Roche NimbleGen scales the ratios in the .gff files by subtracting the bi-weight mean for the log-ratio values from each log-ratio value. If you would like more information about how to calculate a Tukey bi-weight mean scaling please go to Bi-Weight Scale.
Why does Roche NimbleGen use Tukey's bi-weight function for scaling ChIP-chip data? RMA looks at all the arrays in a set and normalizes the data for all the arrays. ChIP-chip is a two color array with the reference on the array and is therefore thought of as a stand alone experiment. RMA is not an appropriate analysis for ChIP chip data. The Tukey bi-weight function is used to account for differences in the dyes on the array, whereas RMA is used to account for differences between arrays so that the arrays can be compared.
Are there any statistical tests that are applied to my ChIP-chip data? Yes, we determine the false discovery rate (FDR) for each peak identified from the scaled log2-ratio data. First the scaled log2-ratio data is analyzed to identify peaks above a specified cutoff value. Assume we find 20 peaks that are above this cutoff value; the scaled log2-ratio data is then randomized 20 different times and after each permutation it is determined how many peaks are still above the cutoff value. So, if after randomizing the data 20 times we find that there are 2 peaks above the cutoff value, the FDR is 10% (which is a reasonably good FDR value). FDR values can differ depending on the peak height and number of probes comprising the peak. On SignalMap, the peaks will be color coded corresponding to FDR value for quick identification of statistically significant peaks.
Other than the pair files, does Roche NimbleGen supply any other raw data files? No, pair files are the only raw data files that Roche NimbleGen includes in delivered ChIP-chip data.
What are the background measurements for a ChIP-chip array? For any ChIP-chip array, the signal is a mix of non-specific signal, “background”, and specific signal. The information given from random probes do not represent true background measurements, but rather non-specific binding events. Currently, we do not calculate background.
Is there another way to analyze ChIP-chip data? Yes, the following five sites have been developed to analyze ChIP-chip data.
1. M-peak: Nature. 2005 436(7052):876-80
2.TAMALPAIS Server: 2006 Genome Research 16:595.
3.ACME (in R language): Methods Enzymol. 2006;411:270-82.
4.ChIPOTle: Genome Biology 2005, 6:R97. For the Perl version, go to ChIPOTle Peak Finder
5.Model-based Analysis of 2-Color Arrays MA2C.
Service Deliverables
Can I get the images for my data? Yes, we can supply the raw data array images (.tif) upon request. Scaled log2-ratio data (.gff) files and peak (.gff) files are included in your deliverable data.
Can I get a graphical representation of all probes for a catalog design so I can see what regions of the genome have coverage? Yes, we can generate this information in GFF for all of catalog designs. You will need a copy of Roche NimbleGen's SignalMap software to view the GFF files. A free, 30-day demo version of SignalMap is available for download.
Does Roche NimbleGen generate reports listing the most significant binding/modification events for my ChIP-chip experiment? Yes, we are including two promoter reports that map the peaks from your ChIP-chip data relative to the transcription start site of a gene. For instance, if a peak is called within the promoter region of a gene, the report lists the approximate location of the peak as a negative position (upstream of the start site) or positive position (downstream). Also listed are accession number of the gene, gene ID, chromosome position, among others. These reports narrow the genomic regions to look at when moving forward to validate your ChIP-chip data (e.g. gel mobility shift assay).
Capabilities
What if a customer has non-nucleosome samples that have an average length of <200bp? If non-nucleosome samples are <200bp, we utilize 7mer random primers to label DNA. However, at this time such samples will be marked as “at risk” because there has not been sufficient validation using 7mers for non-nucleosome samples.
Can I use NimbleGen ChIP-chip to map DNase I hypersensitive sites? Yes, NimbleGen ChIP-chip arrays can be used to map DNase I hypersensitive sites. A manuscript by Crawford et al. (2006. Nature Methods. 3:503-509) describes the use of NimbleGen tiled arrays to map hypersensitive sites. Other manuscripts mapping hypersensitive sites using NimbleGen arrays include Sabo et al. (2006. Nature Methods. 3:511-518) and Follows et al. (2006. Genome Research. 16:1310-1319).
 

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