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Platform GPL15622 Query DataSets for GPL15622
Status Public on Jul 01, 2012
Title NimbleGen Mouse CGH 385K Array [090128_Montreal_JRL_CGH]
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Mus musculus
Manufacturer Roche NimbleGen Inc.
Manufacture protocol See www.nimblegen.com
 
Description Genome Build: NCBI37, MM9

This array type was designed from mm9 and uses c57bl/6 mouse strain chr 6 sequence (~2Mbp) from chr6 and also uses ~700kb of sequence from the 129 mouse strain for the NKC region.

The probes in the .ndf file are designated as _b6 or _129 depending on the origin of the sequence.

The 60bp probes on the array overlap one another by 45bp (i.e. there are 15bp increments in the position of each probe).

For the 129 sequence coordinates, they are derived from the following contigs in Genbank: AY686474, AY686475, AY686476, AY686477, AY686478, which were published as part of this paper: http://www.ncbi.nlm.nih.gov/pubmed/15674375
The sequences of the assembled contig used are provided in the '129-Ly49_total.txt' file.

Since all of the probes appear twice one the array (ie. replicated), unique identifiers were assigned by appending X (ROW) and Y (COL) coordinates on the .NDF file to each probe_ID.

DesignID: 9080

NimbleGen description files linked below:
native array description file: 090128_Montreal_JRL_CGH.ndf
native array description file: Andrew_corrected_posfile.pos
 
Submission date May 28, 2012
Last update date Jul 01, 2012
Contact name Brian Wilhelm
E-mail(s) brian.wilhelm@umontreal.ca
Organization name University of Montreal
Street address 2950 Chemin Polytechnique
City Montreal
ZIP/Postal code H1J 3R4
Country Canada
 
Samples (2) GSM940709, GSM940710
Series (1)
GSE38372 Impaired Natural Killer Cell Self-Education and 'Missing-Self' Responses in Ly49-Deficient Mice

Data table header descriptions
ID unique ProbeID_X_Y (ROW_NUM and COL_NUM)
PROBE_ID NimbleGen probe identifier from .pos file
CHROMOSOME Chromosome number
RANGE_GB Chromosome ACCESSION.VERSION
Chr_strain chromosome_strain
RANGE_START POSITION. Probe start position
RANGE_END POSITION. Probe end position
PROBE_COUNT The uniqueness count of the probe in the target genome
LENGTH Probe length
SEQUENCE Probe oligonucleotide sequence

Data table
ID PROBE_ID CHROMOSOME RANGE_GB Chr_strain RANGE_START RANGE_END PROBE_COUNT LENGTH SEQUENCE
129_1_498_192 129_1 ch6 chr6_129 16 75 1 60 AATTTCCTACAGCCTATTCCAAATCTGAAGCTGAGGAAATTCAGTACCTCATTTTTCTAG
129_2_541_675 129_2 ch6 chr6_129 31 90 1 60 ATTCCAAATCTGAAGCTGAGGAAATTCAGTACCTCATTTTTCTAGTTGTCCTGCTAAGGA
129_3_508_932 129_3 ch6 chr6_129 46 105 1 60 CTGAGGAAATTCAGTACCTCATTTTTCTAGTTGTCCTGCTAAGGACACTGGTTTTGCTCT
129_4_382_90 129_4 ch6 chr6_129 61 120 1 60 ACCTCATTTTTCTAGTTGTCCTGCTAAGGACACTGGTTTTGCTCTCTCTGGAGGAGTGTT
129_5_146_422 129_5 ch6 chr6_129 76 135 1 60 TTGTCCTGCTAAGGACACTGGTTTTGCTCTCTCTGGAGGAGTGTTCCTCCTCTCAGTCTT
129_6_371_991 129_6 ch6 chr6_129 91 150 1 60 CACTGGTTTTGCTCTCTCTGGAGGAGTGTTCCTCCTCTCAGTCTTCCAGTATCAGTTGTG
129_7_43_939 129_7 ch6 chr6_129 106 165 1 60 CTCTGGAGGAGTGTTCCTCCTCTCAGTCTTCCAGTATCAGTTGTGGACATTTCTTTTGTA
129_8_488_54 129_8 ch6 chr6_129 121 180 1 60 CCTCCTCTCAGTCTTCCAGTATCAGTTGTGGACATTTCTTTTGTAGCATCTGGCACATGT
129_9_438_4 129_9 ch6 chr6_129 136 195 1 60 CCAGTATCAGTTGTGGACATTTCTTTTGTAGCATCTGGCACATGTTATTTCTTTCCTTTT
129_10_607_199 129_10 ch6 chr6_129 151 210 1 60 GACATTTCTTTTGTAGCATCTGGCACATGTTATTTCTTTCCTTTTCTCTCAGAGCCAGCT
129_11_607_137 129_11 ch6 chr6_129 166 225 1 60 GCATCTGGCACATGTTATTTCTTTCCTTTTCTCTCAGAGCCAGCTAACTTTCTTTAAGCA
129_12_684_566 129_12 ch6 chr6_129 181 240 1 60 TATTTCTTTCCTTTTCTCTCAGAGCCAGCTAACTTTCTTTAAGCAATTTCCTTTTTTCGG
129_13_116_402 129_13 ch6 chr6_129 196 255 1 60 CTCTCAGAGCCAGCTAACTTTCTTTAAGCAATTTCCTTTTTTCGGTTTGTTTAAGAGGAA
129_14_422_928 129_14 ch6 chr6_129 211 270 1 60 AACTTTCTTTAAGCAATTTCCTTTTTTCGGTTTGTTTAAGAGGAAGAGCAGAAAATCATA
129_15_364_454 129_15 ch6 chr6_129 226 285 1 60 ATTTCCTTTTTTCGGTTTGTTTAAGAGGAAGAGCAGAAAATCATAAGTTTGAGTATTATT
129_16_705_685 129_16 ch6 chr6_129 241 300 1 60 TTTGTTTAAGAGGAAGAGCAGAAAATCATAAGTTTGAGTATTATTCAGAGGAAATTTAAT
129_17_95_701 129_17 ch6 chr6_129 256 315 1 60 GAGCAGAAAATCATAAGTTTGAGTATTATTCAGAGGAAATTTAATTCTGCCTTTCTTCTT
129_18_141_101 129_18 ch6 chr6_129 271 330 1 60 AGTTTGAGTATTATTCAGAGGAAATTTAATTCTGCCTTTCTTCTTGTAACCTCTTACAGG
129_19_294_354 129_19 ch6 chr6_129 286 345 1 60 CAGAGGAAATTTAATTCTGCCTTTCTTCTTGTAACCTCTTACAGGATACAGACAAGGAAA
129_20_54_188 129_20 ch6 chr6_129 301 360 1 60 TCTGCCTTTCTTCTTGTAACCTCTTACAGGATACAGACAAGGAAAGCCAAATTGTCCCCC

Total number of rows: 320162

Table truncated, full table size 41950 Kbytes.




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

Supplementary file Size Download File type/resource
GPL15622_090128_Montreal_JRL_CGH.ndf.gz 15.5 Mb (ftp)(http) NDF
GPL15622_129-Ly49_total.txt.gz 291.0 Kb (ftp)(http) TXT
GPL15622_Andrew_corrected_posfile.pos.gz 946.4 Kb (ftp)(http) POS

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