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Status
Public on May 22, 2011
Title
NimbleGen Bos taurus UMD3.0 2.1M WG HD CGH
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Bos taurus Manufacturer
NimbleGen Systems, Inc.
Manufacture protocol
Maskless array synthesis was used to construct isothermal arrays. 2.1M high density probes were selected with an approximate probe spacing of 1.2 kb. Probes were synthesized using an isothermal format (Tm = 76°C) and varied in length from 50 to 75 bp.
Description
This array was designed based on Btau_UMD3.0.http://www.cbcb.umd.edu/research/bos_taurus_assembly.shtml .
Contributor(s)
Liu GE Submission date
Dec 14, 2010
Last update date
Dec 27, 2010
Contact name
George Liu
E-mail(s)
George.Liu@ars.usda.gov Phone
1-301-504-9843
Fax
1-301-504-8414
Organization name
United States Department of Agriculture
Lab
Bovine Functional Genomics Lab.
Street address
10300 Baltimore Ave
City
Beltsville
State/province
MD
ZIP/Postal code
20705-2350
Country
USA
Samples (80)
GSM641537 , GSM641538 , GSM641548 , GSM641563 , GSM641565 , GSM641566
GSM641588 ,
GSM641632 ,
GSM641633 ,
GSM768564 ,
GSM768572 ,
GSM768575 ,
GSM768580 ,
GSM768596 ,
GSM1537652 ,
GSM1537653 ,
GSM1537654 ,
GSM1537655 ,
GSM1537656 ,
GSM1537657 ,
GSM1537658 ,
GSM1537659 ,
GSM1537660 ,
GSM1537661 ,
GSM1537662 ,
GSM1537663 ,
GSM1537664 ,
GSM1537665 ,
GSM1537666 ,
GSM1537667 ,
GSM1537668 ,
GSM1537669 ,
GSM1537670 ,
GSM1537671 ,
GSM1537672 ,
GSM1537673 ,
GSM1537674 ,
GSM1537675 ,
GSM1537676 ,
GSM3467066 ,
GSM3467067 ,
GSM3467068 ,
GSM3467069 ,
GSM3467070 ,
GSM3467071 ,
GSM3467072 ,
GSM3467073 ,
GSM3467074 ,
GSM3467075 ,
GSM3467076 ,
GSM3467077 ,
GSM3467078 ,
GSM3467079 ,
GSM3467080 ,
GSM3467081 ,
GSM3467082 ,
GSM3467083 ,
GSM3467084 ,
GSM3467085 ,
GSM3467086 ,
GSM3467087 ,
GSM3467088 ,
GSM3467089 ,
GSM3467090 ,
GSM3467091 ,
GSM3467092 ,
GSM3467093 ,
GSM3467094 ,
GSM3467095 ,
GSM3467096 ,
GSM3467097 ,
GSM3467098 ,
GSM3467099 ,
GSM3467100 ,
GSM3467101 ,
GSM3467102 ,
GSM3467103 ,
GSM3467104 ,
GSM3467105 ,
GSM3467106 Series (4)
GSE26132 Assessment of genome integrity with array CGH of cattle transgenic cell lines produced by homologous recombination and somatic cell cloning
GSE31018 Copy number variation of individual cattle genomes using next-generation sequencing.
GSE62990 Next generation sequencing reveals the diversity and population-genetic properties of cattle CNVs
GSE122478 Genome-Wide Detection of CNVs and Their Association with Complex Traits in Holsteins
Data table header descriptions ID CHROMOSOME Chromosome location
RANGE_GB GenBank accession of chromosome
DESIGN_REGION The designed region in which the probes were requested
RANGE_START The start position of the probe relative to RANGE_GB
RANGE_END The end position of the probe relative to RANGE_GB
PROBE_LENGTH The length of probe
SEQUENCE The sequence of probe
Data table ID CHROMOSOME RANGE_GB DESIGN_REGION RANGE_START RANGE_END PROBE_LENGTH SEQUENCE CHR01FS000000021
chr1
GK000001.2 chr1:1-158337067
21
77
57
TTGGAAAGAGAGGAAGTCAAATAACAAAGAAGAGGAAACCACTCTAGAAGTGACAGA
CHR01FS000001168
chr1
GK000001.2 chr1:1-158337067
1168
1217
50
AGTTCCACCGACCAGAACACAGATGCAAGTTTCCCTATCTATGAAAGCTT
CHR01FS000002329
chr1
GK000001.2 chr1:1-158337067
2329
2382
54
ACCTTAAAAGTAAGTGGGTTGGATACCTCAACCAAAAGACAATGACTGACTGAA
CHR01FS000003689
chr1
GK000001.2 chr1:1-158337067
3689
3741
53
AGCCCAGGACAAGATGGCTTCACGGGTGAATTTTACCAAAATTTTAGAGAAGA
CHR01FS000005429
chr1
GK000001.2 chr1:1-158337067
5429
5486
58
TACAAGCAGTTCATGCAAGTCAATACCAGAAATTAAGTGACCAAATAAAAAAATGGGC
CHR01FS000006649
chr1
GK000001.2 chr1:1-158337067
6649
6706
58
CCATTGACAGAAGGACGCTGGAAATCACCAAGAAAAGATACAACACATCCAAAGAAAA
CHR01FS000008649
chr1
GK000001.2 chr1:1-158337067
8649
8698
50
ATCTTCTGCTTTTGTCAGACCAACCTGCTAATGTTGGAGGGTCTCCTGTG
CHR01FS000009554
chr1
GK000001.2 chr1:1-158337067
9554
9603
50
AAGTTTAGGAAGTGCAAAGAGTCCCAGGCAGGATAAACCTAAGGAGGAAC
CHR01FS000011524
chr1
GK000001.2 chr1:1-158337067
11524
11581
58
AATAGGAAAATTTGTAATCACTTCTTAATATCCAGATGTGTACCACAATTATCTTGGA
CHR01FS000012649
chr1
GK000001.2 chr1:1-158337067
12649
12698
50
CCTTTAGACCAGGAAGTTTCTGGACCTAGTCCTATCTCCCTGGACATATT
CHR01FS000013868
chr1
GK000001.2 chr1:1-158337067
13868
13917
50
AAGTAAGTGATGTGCCAATATCCGCATACTTTCCTAGGGACGTATGTGGT
CHR01FS000014863
chr1
GK000001.2 chr1:1-158337067
14863
14912
50
AAATGATACAGTCAAATGCACATCACAGGTCTCTCAACTGCTGGCACTGG
CHR01FS000016047
chr1
GK000001.2 chr1:1-158337067
16047
16096
50
TTCTGACACTTCATAGAGAATCACCACCCACTCACAGATGTGAGTCAGAA
CHR01FS000017332
chr1
GK000001.2 chr1:1-158337067
17332
17393
62
TTTCACCTTAAAATCTGGATCCTCTAGAACTCCTGTTGCTCTATCTTATCATCTTGAAGAGA
CHR01FS000018442
chr1
GK000001.2 chr1:1-158337067
18442
18493
52
TCTATAGCATTTTGTTTGAGGATCGACTTTGTGGAGAGAGCAACAGGGAATG
CHR01FS000019628
chr1
GK000001.2 chr1:1-158337067
19628
19677
50
GGGTGTGTGGGTGCTTATTGTGGTTGCAGGTACTATTGTAGTTAGTCTCA
CHR01FS000020533
chr1
GK000001.2 chr1:1-158337067
20533
20582
50
ACAGACGACAGACACAAGTTCGCCAGCAAGAGCCAGAGTCATAGCACCTA
CHR01FS000021793
chr1
GK000001.2 chr1:1-158337067
21793
21857
65
AATATTCTCAGAGGCAATATGTGAGAGATCTAATTTTGCTACATCGTTGCTACTGTCACCATTTA
CHR01FS000022946
chr1
GK000001.2 chr1:1-158337067
22946
22995
50
AATAAAGACAACATGGACAACCTGCCACGGCCAACGACATAAGTCCCTAA
CHR01FS000024207
chr1
GK000001.2 chr1:1-158337067
24207
24266
60
ACAGAAATGGAAGTAAGATGACAGAGACTCAAATTACAAACTATGATCATCTTTAAAGGA
2166464 267976 Kbytes .Supplementary file Size Download File type/resource GPL11314_Btau_4.0.txt.gz
24.6 Mb
(ftp) (http) TXT
GPL11314_Btau_UMD3_CGH_HX1.ndf.gz
120.3 Mb
(ftp) (http) NDF
GPL11314_Btau_UMD3_CGH_HX1.pos.gz
16.9 Mb
(ftp) (http) POS
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