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Platform GPL16801 Query DataSets for GPL16801
Status Public on Mar 18, 2013
Title NimbleGen Nasonia vitripennis 1.0 Whole-genome Tiling Array Set (2 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 (2 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_2.ndf
Native array description file: 080222_Nvit1_JC_ChIP_HX1_2.pos
Native array description file: 080222_Nvit1_JC_ChIP_HX1_2.ncd

The GenBank and RefSeq accessions.version for the scaffolds in the .pos file are available in the supplementary file 'GPL16801_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) GSM1123051, GSM1123052, GSM1123053, GSM1123063, GSM1123064, GSM1123065 
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
SCAFFOLD24FS001411327 7159 7159_1_1 SCAFFOLD24:1-2507974 1411327 ATCAATTACATATTCGCATCGCGCAGAAGATTGGCTCGTCTATACAAACCAG
SCAFFOLD25FS000698790 7159 7159_1_3 SCAFFOLD25:1-1572414 698790 CAACTCTTGTTTACACCCTCGCGCGACTCTGCCAGGGGGCAGCTCGTCGC
SCAFFOLD21FS001321302 7159 7159_1_5 SCAFFOLD21:1-2981920 1321302 TCATATTCGCCCGTCCTGTATAAAGACGCTCGTATGCCGTCTCTATACGT
SCAFFOLD23FS001023598 7159 7159_1_7 SCAFFOLD23:1-2418722 1023598 AATAGGTGAGGATTTAACATTCGCGCGCGGCGTTATTTTCATTTGCCGTTAATAG
SCAFFOLD22FS001061971 7159 7159_1_9 SCAFFOLD22:1-2677829 1061971 TTCGGTTTTGATTCTCTATATTTATACGTAACTCAGTGTACGGGGTGTGCGC
SCAFFOLD23FS001974148 7159 7159_1_11 SCAFFOLD23:1-2418722 1974148 GTTATACATTACTGGCTTTACTGCAGCTTATTTTTCTCTCAGGAGAGCTCCGATTTTGAA
SCAFFOLD24FS001049548 7159 7159_1_13 SCAFFOLD24:1-2507974 1049548 ATCTCTAATAACGCCGCCAGCGCGCGCGTACAGCGCCATAAATAACCGAA
RANDOM00045115 7159 7159_1_15 RANDOM_MK1 0 CGATGCGCTACGCTGATCCGAAGAAAATGGTCGGGAATGCGTAGATCGTTTAGAAGAAT
SCAFFOLD26FS000055152 7159 7159_1_17 SCAFFOLD26:1-1596276 55152 TATACCTTTATGCCGACGCGATTCTTAATTGATCGGTGCGGCTGTATAAGA
SCAFFOLD20FS001249425 7159 7159_1_19 SCAFFOLD20:1-2035339 1249425 TATAGCCAACACACGCGCGGCGACGATTTATTCGCGTCTATCGGTCTATC
SCAFFOLD23FS000281276 7159 7159_1_21 SCAFFOLD23:1-2418722 281276 TTTCCTGGCTCTTAACTCTTTCCATCCCACCTCGTTTCTCCGCTTGCCAA
SCAFFOLD23FS000662736 7159 7159_1_23 SCAFFOLD23:1-2418722 662736 GCATGCCTTTTTCCTTGTATACTCGTTGTATTTCTTTTTCTCTCAATCAGATTGAGAGCCA
SCAFFOLD21FS001607099 7159 7159_1_25 SCAFFOLD21:1-2981920 1607099 CTCTGTCCTCAAAACCAAAGTTCTTAGTCAACAGTTAAAATTTTAAAATATA
SCAFFOLD27FS000093520 7159 7159_1_27 SCAFFOLD27:1-1641043 93520 AATAAGAAGCCGCGCAACGCGTGAGTACAGTCATCCACCCTGCGTACCAC
SCAFFOLD27FS001028872 7159 7159_1_29 SCAFFOLD27:1-1641043 1028872 TGTGTGTGTGCACGTGAAGTAGGAAAAGCAGGGGAATCGAGCGACAGCAG
SCAFFOLD22FS002529770 7159 7159_1_31 SCAFFOLD22:1-2677829 2529770 ATCTTAACAAGCCGCACACAGGCGTGTCCCGAGAAGTGTCGCCCTCTGTC
SCAFFOLD24FS001104637 7159 7159_1_33 SCAFFOLD24:1-2507974 1104637 CGGGCGCGTATAGGCCGCACATATTCCACGGGGGCGAAGCAGCCTGCACG
SCAFFOLD28FS000114780 7159 7159_1_35 SCAFFOLD28:1-1899952 114780 TATTATTATTATCACCGCTGTACCCTGGCTTTCGAGAGGATTTGCCTTTTAGTTTG
SCAFFOLD27FS000143736 7159 7159_1_37 SCAFFOLD27:1-1641043 143736 GAATTATCCCAATTACAGAGATAAAAAAAACGGAATGCCTCCTTATGCGGAGCATTA
SCAFFOLD23FS000622539 7159 7159_1_39 SCAFFOLD23:1-2418722 622539 TGCGATTGTGCGATTTTGTGGGAGCACTTGTATATAACACTTATCTCCGC

Total number of rows: 2160888

Table truncated, full table size 259713 Kbytes.




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Supplementary file Size Download File type/resource
GPL16801_080222_Nvit1_JC_ChIP_HX1_2.ncd.gz 264 b (ftp)(http) NCD
GPL16801_080222_Nvit1_JC_ChIP_HX1_2.ndf.gz 114.0 Mb (ftp)(http) NDF
GPL16801_080222_Nvit1_JC_ChIP_HX1_2.pos.gz 15.7 Mb (ftp)(http) POS
GPL16801_accessions_for_array_set.txt.gz 64.7 Kb (ftp)(http) TXT

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