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Platform GPL18665 Query DataSets for GPL18665
Status Public on May 09, 2014
Title NimbleGen Triticum aestivum CGH 270K array [120227_Taest_SRS_CGH]
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Triticum aestivum
Manufacturer NimbleGen
Manufacture protocol http://www.nimblegen.com
 
Description Custom 12x270k CGH probe layout for Triticum aestivum (wheat) chromosome 7B probes provided by the customer. 67,500 experimental probes were added to the array in four replicate probe sets (BLOCK1-BLOCK4). No chromosome positions were provided so no POS, GFF or GCSTATS files could be created. Empty features on the array were filled with randomly generated probes of comparable length and composition.

DESIGN_ID: 566481
design name: 120227_Taest_SRS_CGH

native array description file: 120227_Taest_SRS_CGH.ndf
native array description file: 120227_Taest_SRS_CGH_UX12.ncd

Platform Columns file:DesignFile.pdf
 
Submission date May 08, 2014
Last update date May 09, 2014
Contact name Tatiana Belova
E-mail(s) tatiana.belova@nmbu.no
Organization name cigene
Department department of plant science
Lab department of plant science
Street address arboretveien 6
City Aas
State/province none
ZIP/Postal code 1430
Country Norway
 
Samples (22) GSM1383116, GSM1383117, GSM1383118, GSM1383119, GSM1383120, GSM1383121 
Series (1)
GSE57461 High-density deletion bin map of wheat chromosome 7B

Data table header descriptions
ID PROBE_DESIGN_ID consisting DESIGN_ID, ROW_NUM, COL_NUM
CONTAINER NimbleGen identifier, supplied by NimbleGen
SPOT_ID SEQ_ID
SEQUENCE Sequence of probe
MISMATCH the mismatch index of the PROBE_SEQUENCE. "0" for the perfect match
MATCH_INDEX same as feature id
FEATURE_ID Unsigned integer that uniquely identifies a feature
ROW_NUM The row within the grid in which the feature is located.
COL_NUM The column within the grid in which the feature is located.
PROBE_CLASS The type of probe, usually experimental or control
PROBE_ID ID of the prob
POSITION no chromosome position avalable
X The DLP X coordinate of the feature on the image
Y The DLP Y coordinate of the feature on the image

Data table
ID CONTAINER SPOT_ID SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS PROBE_ID POSITION X Y
566481_0001_0001 NGS_CONTROLS CROSSHYBE TAGCGTTGCTTAGGCGTACGCAGTCTGATGCGTCGTTAGCATCGGCAANNNNNNNNNN 0 14538087 14538087 1 1 control:crosshybe XENOTRACK48P01 1 1 1
566481_0002_0001 NGS_CONTROLS EMPTY N 0 14538088 14538088 1 2 control:empty EMPTY 0 2 1
566481_0003_0001 NGS_CONTROLS CROSSHYBE CGATGCGACGCGAACTAAGCAGTTCGGCGCAGTCGACTAGTATAACAGNNNNNNNN 0 14538089 14538089 1 3 control:crosshybe XENOTRACK48P02 2 3 1
566481_0004_0001 NGS_CONTROLS EMPTY N 0 14538090 14538090 1 4 control:empty EMPTY 0 4 1
566481_0005_0001 NGS_CONTROLS CROSSHYBE GTCGCAACGAGTTAGCGTGATCGACTTGACTGCGTACGCACAGCAATGNNNNNNNNNN 0 14538091 14538091 1 5 control:crosshybe XENOTRACK48P03 3 5 1
566481_0006_0001 NGS_CONTROLS EMPTY N 0 14538092 14538092 1 6 control:empty EMPTY 0 6 1
566481_0007_0001 NGS_CONTROLS CROSSHYBE CTGAGCGATACGCGTTAACCAGGCCGGTCGTATCAGATACGCATTCGGNNNNNNN 0 14538093 14538093 1 7 control:crosshybe XENOTRACK48P04 4 7 1
566481_0008_0001 NGS_CONTROLS EMPTY N 0 14538094 14538094 1 8 control:empty EMPTY 0 8 1
566481_0009_0001 NGS_CONTROLS CROSSHYBE CATGACACGGAGTAAGCGAGCCTACAGCGAGCATAATGATCGGCTAGCNNNNNNNNNNN 0 14538095 14538095 1 9 control:crosshybe XENOTRACK48P05 5 9 1
566481_0010_0001 NGS_CONTROLS EMPTY N 0 14538096 14538096 1 10 control:empty EMPTY 0 10 1
566481_0011_0001 NGS_CONTROLS CROSSHYBE CCTCGTAAGCTTGACGTGCACTCGGTCCGGAATCACGTACGTCGGCTANNNNNN 0 14538097 14538097 1 11 control:crosshybe XENOTRACK48P06 6 11 1
566481_0012_0001 NGS_CONTROLS EMPTY N 0 14538098 14538098 1 12 control:empty EMPTY 0 12 1
566481_0013_0001 NGS_CONTROLS CROSSHYBE GCGTATGAATCGCGGATAGGCATGCCGTAAGCGAGCTAGAACGAATGGNNNNNNNNN 0 14538099 14538099 1 13 control:crosshybe XENOTRACK48P07 7 13 1
566481_0014_0001 NGS_CONTROLS EMPTY N 0 14538100 14538100 1 14 control:empty EMPTY 0 14 1
566481_0015_0001 NGS_CONTROLS CROSSHYBE CCGCGTGCAATTATCGGAGTCTAGCGGAAGTACACAACTCGGTCGTTGNNNNNN 0 14538101 14538101 1 15 control:crosshybe XENOTRACK48P08 8 15 1
566481_0016_0001 NGS_CONTROLS EMPTY N 0 14538102 14538102 1 16 control:empty EMPTY 0 16 1
566481_0017_0001 NGS_CONTROLS CROSSHYBE CCGTTGAGTAACGTCGAGCGTTAGGTCTCAGCGTAAGCGTCGATAACGNNNNN 0 14538103 14538103 1 17 control:crosshybe XENOTRACK48P09 9 17 1
566481_0018_0001 NGS_CONTROLS EMPTY N 0 14538104 14538104 1 18 control:empty EMPTY 0 18 1
566481_0019_0001 NGS_CONTROLS CROSSHYBE CGCGCGTGAGTATATATGCACTGCGGCCGTATATTATAAGGCGCCACGNNNNNNNNN 0 14538105 14538105 1 19 control:crosshybe XENOTRACK48P10 10 19 1
566481_0020_0001 NGS_CONTROLS EMPTY N 0 14538106 14538106 1 20 control:empty EMPTY 0 20 1

Total number of rows: 291410

Table truncated, full table size 45257 Kbytes.




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

Supplementary file Size Download File type/resource
GPL18665_120227_Taest_SRS_CGH.ndf.gz 12.6 Mb (ftp)(http) NDF
GPL18665_120227_Taest_SRS_CGH_UX12.ncd.gz 314 b (ftp)(http) NCD
GPL18665_DesignFile.pdf.gz 9.0 Kb (ftp)(http) PDF

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