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Platform GPL9799 Query DataSets for GPL9799
Status Public on Jun 11, 2010
Title NimbleGen 385k whole genome tiling 2006-07-12_galGal3_WG_CGH
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Gallus gallus
Manufacturer NimbleGen
Manufacture protocol Whole genome CGH design for chicken (galGal3). Whole genome tiled at 50 bp interval spacing using dual mode (Tm 76; 148 cycles). Whole genome CGH probes selected at 2000 bp interval spacing, using 500 bp window. Used 15mer frequency of 30 for final filtering. Interval spacing stats: 2557 bp (mean); 2586 bp (median). 4357 random probes added.
 
Description UCSC May 2006 chicken (Gallus gallus) v2.1 draft assembly
 
Submission date Dec 14, 2009
Last update date Jun 11, 2010
Contact name Xiaofei Wang
E-mail(s) xwang@tnstate.edu
Phone 615 963 2541
Organization name Tennessee State University
Department Biological Sciences
Street address 3500 John A Merritt blvd
City Nashville
State/province TN
ZIP/Postal code 37209
Country USA
 
Samples (26) GSM485166, GSM485167, GSM485168, GSM485169, GSM485170, GSM485171 
Series (3)
GSE19469 An initial map of chromosomal segmental copy number variations in chickens
GSE38689 Genome-wide copy number variant analysis in inbred lines of chickens with different susceptibility to Marek’s disease
GSE49889 Identification of copy number variation using aCGH in Chinese chicken breeds

Data table header descriptions
ID
GB_RANGE RefSeq Assembly Accession [start..stop]
CHROMOSOME
SEQ_ID
POSITION
LENGTH
GC
SEQUENCE

Data table
ID GB_RANGE CHROMOSOME SEQ_ID POSITION LENGTH GC SEQUENCE
CHR01P000005491 NC_006088.2[5491..5540] chr1 chr1 5491 50 0.58 ACCCTTCACCGGTCCGTAGTGGTGAGGGATCGGATGGCAGAAAACCCTCT
CHR01P000027979 NC_006088.2[27979..28028] chr1 chr1 27979 50 0.48 CTTTCCCTTTTCATTGCCATCCTCACACGCACGGAAAGTAGTTTGGCTGT
CHR01P000032959 NC_006088.2[32959..33008] chr1 chr1 32959 50 0.50 ATGGTGCTAATGGCTAAATAGGAATTGCAAGCACCGGGCTGTTTCTGCCC
CHR01P000035209 NC_006088.2[35209..35258] chr1 chr1 35209 50 0.48 GATGCTGAGCCGTTTGTCAGGTTTGGCGAATACTGTTCTACAAGAGCTGT
CHR01P000037709 NC_006088.2[37709..37766] chr1 chr1 37709 58 0.40 TGACCACATCATCTTTTTGGGAAAAACTTTGTATGAGTGGGTAAGAGGAGTGAGATAG
CHR01P000040361 NC_006088.2[40361..40410] chr1 chr1 40361 50 0.42 GAAAAGAAAGGCTTTACAAAGGCGTCCAAGGGAAAGGGAAGAGTTTTATG
CHR01P000042961 NC_006088.2[42961..43012] chr1 chr1 42961 52 0.42 TGTGTTTTATGCCATAGCTGTTGTCTGCATGTCGTGCAATACATCACAGAGT
CHR01P000045014 NC_006088.2[45014..45072] chr1 chr1 45014 59 0.37 AAGTTGCAAACAGTAGGGCAGCTTCTCTCTAACAAATTGAGAGTTCTGCTATGTTTATT
CHR01P000047716 NC_006088.2[47716..47765] chr1 chr1 47716 50 0.50 AGGGCAAAAGTTGGCATTTGGGACTCGCAAGTGCAGAGTCAGTACATCCT
CHR01P000050317 NC_006088.2[50317..50369] chr1 chr1 50317 53 0.42 AGAGACTGTGGATATGATGCCAGTATCTGTAGTCTCGAAATATGGCTGGATAA
CHR01P000052517 NC_006088.2[52517..52566] chr1 chr1 52517 50 0.46 TTCAGGAAGCCCTGGTGTCTCGCAAAGACACTATAAAGAAGGCTCAAGAA
CHR01P000055113 NC_006088.2[55113..55162] chr1 chr1 55113 50 0.44 AGCTGTGCATTCTAAAGAGGACTATCGTGTCACTGCTAATGTGCCTATAG
CHR01P000057913 NC_006088.2[57913..57966] chr1 chr1 57913 54 0.41 TCAGATCCTGTGGACTTAGTATGTGCCATTTGTTACACTCTCTGACATATGGAA
CHR01P000060163 NC_006088.2[60163..60220] chr1 chr1 60163 58 0.40 AGCTTATTTGTATATAATCATAGCGCTCTCCATTCCGAGCTGACAATGAAAGGAACAC
CHR01P000062963 NC_006088.2[62963..63012] chr1 chr1 62963 50 0.44 CCTTAGAAATGGGCACTGTGGCAGCACCTACATACTCAGTAGAATTCTTA
CHR01P000065363 NC_006088.2[65363..65412] chr1 chr1 65363 50 0.46 GCTCAGTCTGGTGTAAGAAAACGTGAACTGAGAACTGTGAGCCTATAGCA
CHR01P000067713 NC_006088.2[67713..67769] chr1 chr1 67713 57 0.40 CTGTGTGCATTTCCTTATGTGTTCATTCCATCGGATCTGTTTCTTCCAATTGAATGC
CHR01P000075333 NC_006088.2[75333..75382] chr1 chr1 75333 50 0.46 ACTGTCTGCAAAATGTGCTTGAACCCATCCACATCATTTGTCCCTGCTGA
CHR01P000077933 NC_006088.2[77933..77982] chr1 chr1 77933 50 0.44 ATCCCAACGAGACAGAGGTGGAAGGAGCACATATCTAGAAACATACTTCT
CHR01P000080433 NC_006088.2[80433..80482] chr1 chr1 80433 50 0.46 GTCAGTTTGTGGCAGCTGGAACAGATTTCAGAAGGAGTAGAATCATCCGA

Total number of rows: 385002

Table truncated, full table size 48836 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary file Size Download File type/resource
GPL9799_2006-07-12_galGal3_WG_CGH.ndf.gz 20.7 Mb (ftp)(http) NDF
GPL9799_2006-07-12_galGal3_WG_CGH.pos.gz 2.9 Mb (ftp)(http) POS

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