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Platform GPL21314 Query DataSets for GPL21314
Status Public on Feb 24, 2016
Title NimbleGen Cynomolgus monkey CGH 4.2M Whole-Genome Tiling Array [120405_Cynomolgus5_CGH_UX1]
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Macaca fascicularis
Manufacturer NimbleGen
Manufacture protocol High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.
 
Description whole-genome tiling array for Macaca fascicularis genome version 5.0 with 4.2 million isothermal tiling oligos with a median spacing of 598bp
Genome build information Macaca fascicularis genome version 5.0 (August 2011) described in Ebeling et al. (2011) Genome Research (PMID: 21862625)
Gene locus and gene annotation in this record is based on 120405_Cynomolgus5_CGH_UX1.gff

native array description file:
120405_Cynomolgus5_CGH_UX1.ndf
120405_Cynomolgus5_CGH_UX1.pos
120405_Cynomolgus5_CGH_UX1.gcstats.txt
120405_Cynomolgus5_CGH_UX1.gff
120405_Cynomolgus5_CGH_UX1_probe_locations.gff
120405_Cynomolgus5_CGH_UX1.ncd

DESIGN NAME: 120405_Cynomolgus5_CGH_UX1
DESIGN_ID: 568661
ORGANISM_GENOME_BUILD=cyno5
http://www.ebi.ac.uk/ena/data/view/GCA_000222185
 
Submission date Jan 08, 2016
Last update date Feb 24, 2016
Contact name Tobias Heckel
E-mail(s) tobias-heckel@t-online.de
Organization name Roche
Department pRED
Lab Safety Genetics & Genomics
Street address Grenzacherstr. 124
City Basel
ZIP/Postal code CH-4070
Country Switzerland
 
Samples (21) GSM2036270, GSM2036271, GSM2036272, GSM2036273, GSM2036274, GSM2036275 
Series (2)
GSE76707 Genome-wide copy number variation profiling in Cynomolgus monkeys using customized NimbleGen CGH microarrays
GSE76708 Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis

Data table header descriptions
ID PROBE_ID from .pos file
SEQ_ID sequence identifier, which is used to group probes into container: e.g. group all chr1-probes to chr1 form locus ID 1 to locus ID 229 594 237
CHROMOSOME Chromosomal location
RANGE_START POSITION. Probe start position in the target sequence or region of interest, starting at the 5' end
RANGE_END Probe end position
LENGTH
GC GC content of the probe

Data table
ID SEQ_ID CHROMOSOME RANGE_START RANGE_END LENGTH GC
CHR01FS000000401 chr1:1-229594237 chr1 401 456 56 0.36
CHR01FS000000916 chr1:1-229594237 chr1 916 965 50 0.56
CHR01FS000001491 chr1:1-229594237 chr1 1491 1548 58 0.36
CHR01FS000002174 chr1:1-229594237 chr1 2174 2223 50 0.58
CHR01FS000002764 chr1:1-229594237 chr1 2764 2821 58 0.40
CHR01FS000003369 chr1:1-229594237 chr1 3369 3418 50 0.44
CHR01FS000003959 chr1:1-229594237 chr1 3959 4008 50 0.44
CHR01FS000004566 chr1:1-229594237 chr1 4566 4615 50 0.50
CHR01FS000005121 chr1:1-229594237 chr1 5121 5170 50 0.50
CHR01FS000005668 chr1:1-229594237 chr1 5668 5717 50 0.56
CHR01FS000006288 chr1:1-229594237 chr1 6288 6337 50 0.62
CHR01FS000006898 chr1:1-229594237 chr1 6898 6947 50 0.56
CHR01FS000007488 chr1:1-229594237 chr1 7488 7537 50 0.64
CHR01FS000008132 chr1:1-229594237 chr1 8132 8181 50 0.44
CHR01FS000008690 chr1:1-229594237 chr1 8690 8739 50 0.50
CHR01FS000009326 chr1:1-229594237 chr1 9326 9375 50 0.46
CHR01FS000009839 chr1:1-229594237 chr1 9839 9889 51 0.43
CHR01FS000010798 chr1:1-229594237 chr1 10798 10860 63 0.38
CHR01FS000011569 chr1:1-229594237 chr1 11569 11618 50 0.54
CHR01FS000012153 chr1:1-229594237 chr1 12153 12202 50 0.58

Total number of rows: 4265809

Table truncated, full table size 275050 Kbytes.




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

Supplementary file Size Download File type/resource
GPL21314_120405_Cynomolgus5_CGH_UX1.gcstats.txt.gz 45.9 Mb (ftp)(http) TXT
GPL21314_120405_Cynomolgus5_CGH_UX1.gff.gz 4.0 Mb (ftp)(http) GFF
GPL21314_120405_Cynomolgus5_CGH_UX1.ncd.gz 266 b (ftp)(http) NCD
GPL21314_120405_Cynomolgus5_CGH_UX1.ndf.gz 243.7 Mb (ftp)(http) NDF
GPL21314_120405_Cynomolgus5_CGH_UX1.pos.gz 33.2 Mb (ftp)(http) POS
GPL21314_120405_Cynomolgus5_CGH_UX1_probe_locations.gff.gz 31.4 Mb (ftp)(http) GFF

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