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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=cyno5http://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
GSM2036276 ,
GSM2036277 ,
GSM2036278 ,
GSM2036279 ,
GSM2036280 ,
GSM2036281 ,
GSM2036282 ,
GSM2036283 ,
GSM2036284 ,
GSM2036285 ,
GSM2036286 ,
GSM2036287 ,
GSM2036288 ,
GSM2036289 ,
GSM2036290
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 .
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