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Platform GPL16800 Query DataSets for GPL16800
Status Public on Mar 18, 2013
Title NimbleGen Nasonia vitripennis 1.0 Whole-genome Tiling Array Set (1 of 4) [080222_Nvit1_JC_ChIP_HX1]
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Nasonia vitripennis
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 This is a Jewel Wasp (Nasonia vitripennis) whole-genome tiling array set (1 of 4) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen. The array is based on assembly Nvit_1.0.

Native array description file: 080222_Nvit1_JC_ChIP_HX1_1.ndf
Native array description file: 080222_Nvit1_JC_ChIP_HX1_1.pos
Native array description file: 080222_Nvit1_JC_ChIP_HX1_1.ncd

The GenBank and RefSeq accessions.version for the scaffolds in the .pos file are available in the supplementary file 'GPL16800_accessions_for_array_set.txt'.
 
Contributor(s) Colbourne JK, Choi JH, Werren J
Submission date Mar 17, 2013
Last update date Apr 15, 2013
Contact name Justin Choi
E-mail(s) jeochoi@gmail.com
Phone 1-706-721-6757
Organization name Georgia Regents University
Department Cancer Center
Street address 1410 Laney Walker Blvd.
City Augusta
State/province GA
ZIP/Postal code 30912
Country USA
 
Samples (18) GSM1123048, GSM1123049, GSM1123050, GSM1123060, GSM1123061, GSM1123062 
Series (7)
GSE44701 Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development
GSE46078 Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Embryo10)
GSE46079 Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Embryo18)

Data table header descriptions
ID Probe_ID
DESIGN_ID NimbleGen design reference
PROBE_DESIGN_ID NimbleGen design reference with Position ID
SEQ_ID Custom sequence ID
POSITION Start position of probe relative to CHROMOSOME in .pos file
SEQUENCE Nucleotide sequence of probe

Data table
ID DESIGN_ID PROBE_DESIGN_ID SEQ_ID POSITION SEQUENCE
SCAFFOLD9FS003408475 7156 7156_1_1 SCAFFOLD9:1-4553683 3408475 TAGAGAGACGCAGACCGCGTTGGCGAAATCGGCAATGCTGATGACGATCA
SCAFFOLD6FS001249540 7156 7156_1_3 SCAFFOLD6:1-4401492 1249540 AGCCGGGCCAACAATACGTGAATTAGTCCTCGACATTAGGCTCCATCCGA
SCAFFOLD7FS001151228 7156 7156_1_5 SCAFFOLD7:1-4040552 1151228 TCTCCGCAATGTAAAACGTTCATTACACCGTCGTATAAGAGAACATATTTACGGC
SCAFFOLD8FS002395129 7156 7156_1_7 SCAFFOLD8:1-3676232 2395129 GGAGAGAGTATATGGTGTGCTGATTCCGCTGCGCCTTAATTATTTAACGG
SCAFFOLD6FS000516814 7156 7156_1_9 SCAFFOLD6:1-4401492 516814 AAATTCTAGACCGCAATTCAACGACGATGAAATCACATTTTCGGCCCAATGAC
SCAFFOLD7FS002788163 7156 7156_1_11 SCAFFOLD7:1-4040552 2788163 GCTATTGTGGACGATTGCTCCTGTAATCGCTAATTAGATGATCTTCGAATAGATCGA
SCAFFOLD6FS002391280 7156 7156_1_13 SCAFFOLD6:1-4401492 2391280 TAATGAGAGTACTCTCGGCGGCGGCCGCAATTAGCGAAAATTTATACCGA
SCAFFOLD8FS003498752 7156 7156_1_15 SCAFFOLD8:1-3676232 3498752 TTTGCAACCATTTTCATTATCATACCGTACCATTTGATTCTGAAAAATATTGTTCGAA
SCAFFOLD6FS002321292 7156 7156_1_17 SCAFFOLD6:1-4401492 2321292 TCGCGTGAATCAGGCAAAAAAAGCCAGTGTGTTTGTAAGCGAATACACTC
SCAFFOLD7FS003042340 7156 7156_1_19 SCAFFOLD7:1-4040552 3042340 TTGGTCCTCGCCAGACGATCCTCTGGACGTCCCTAGTCGCCGCAATAGCT
SCAFFOLD9FS003829792 7156 7156_1_21 SCAFFOLD9:1-4553683 3829792 GAGTATAGGTGCGCGAGTGCCAAAAACCACCGAAATAACTCGGGTCTTGG
SCAFFOLD9FS003869098 7156 7156_1_23 SCAFFOLD9:1-4553683 3869098 TCGCGATACAATTTAAGAGCTGTGCTATGCTGCAGCGCAAATATTGCATAAATCTTTTTCCATTA
SCAFFOLD7FS002457195 7156 7156_1_25 SCAFFOLD7:1-4040552 2457195 TTCATGTGGTGTATAGATTGTTGCTGTAGAGGTTGGAGCGAATGGGAGAAAGTCAAAAATA
SCAFFOLD7FS000624416 7156 7156_1_27 SCAFFOLD7:1-4040552 624416 TGGTATAGCTTTTCGGGAGCATCATCCCTAATTAGGCCGCATTAGATTAG
SCAFFOLD6FS000307859 7156 7156_1_29 SCAFFOLD6:1-4401492 307859 TAAGGAGCCGCGCGAAATATCTCTAATTTTCCACGGCTGATTGGTTAGGC
SCAFFOLD9FS002554953 7156 7156_1_31 SCAFFOLD9:1-4553683 2554953 CGATACGTTTCACAATTCAAATGTGAAAACACGACACTAGAACAAAACAATTGAGTA
SCAFFOLD6FS002073403 7156 7156_1_33 SCAFFOLD6:1-4401492 2073403 CGAGAGACAGCGAGCGACGCCGAGTAGGCCCATTCACGGGCTCGGATTCC
SCAFFOLD6FS000829425 7156 7156_1_35 SCAFFOLD6:1-4401492 829425 CGTTGCCTTCAAATGGGTTAGACGAGAACTGAACGAATCAGTGTTTTGTACTTT
SCAFFOLD9FS002007410 7156 7156_1_37 SCAFFOLD9:1-4553683 2007410 GTGATTTCTGACATTTGAAGACTACTGTAAAATGAAGACGTTTGCGGTCGTTTTAG
SCAFFOLD8FS002524877 7156 7156_1_39 SCAFFOLD8:1-3676232 2524877 ACGTACAAGATATCCGCGAGCGGGAACATAAGATCGGTGTGGTTTTTTCC

Total number of rows: 2160888

Table truncated, full table size 256128 Kbytes.




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Supplementary file Size Download File type/resource
GPL16800_080222_Nvit1_JC_ChIP_HX1_1.ncd.gz 264 b (ftp)(http) NCD
GPL16800_080222_Nvit1_JC_ChIP_HX1_1.ndf.gz 112.8 Mb (ftp)(http) NDF
GPL16800_080222_Nvit1_JC_ChIP_HX1_1.pos.gz 15.7 Mb (ftp)(http) POS
GPL16800_accessions_for_array_set.txt.gz 64.7 Kb (ftp)(http) TXT

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