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Platform GPL10758 Query DataSets for GPL10758
Status Public on Apr 12, 2011
Title Mussel Immunochip 1.0
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Mytilus galloprovincialis
Manufacturer Department of Biology and C.R.I.B.I. (University of Padova)
Manufacture protocol Immunochip 1.0 includes 1820 spotted oligonucleotides representing putative immune-related transcripts of M. galloprovincialis. The probe ID also indicates the related transcript sequence available at http://mussel.cribi.unipd.it. For instance, MGO_00175 relates to MGC00175 in Mytibase, a dynamic knowledgebase of expressed mussel sequences described in BMC Genomics 2009 Feb 9;10:72. Probes were designed with OligoArray 2.1. Additional 38 oligonucleotides, with no virtual hybridization against the whole mussel EST collection, were similarly prepared from human sequences.
The probe set was arranged and deposited twice (BioRobotics MicroGrid II, Digilab, Genomic Solutions) on derivatized glass slides (MICROMAX Glass Slides: SuperChip I, Perkin-Elmer) at 50% relative humidity. Each array is organized in 16 subarrays and contains 4x1820 mussel probes, 652 unrelated probes in multiple replicates and 112 alignment spots. Probe fixation on slide was performed with a UV cross linker (Stratagene). Slides were rinsed once in 1% SDS, 3× SSC for 1 min at room temperature, twice in distilled water for 5 min at room temperature and than dried in a laminar flux chamber.
Support glass
Coating aminosilane
 
 
Web link http://microcribi.cribi.unipd.it
Contributor(s) Varotto L, Rosani U, Bernante F, Cagnin S, Lanfranchi G, Pallavicini A, Venier P
Citation(s) 21269501
Submission date Aug 04, 2010
Last update date Apr 12, 2011
Contact name Laura Varotto
E-mail(s) lauravarotto@yahoo.it
Phone 00390498276284
Organization name University of Padova
Department Biology Department
Street address via U. Bassi 58/3
City Padova
ZIP/Postal code 35121
Country Italy
 
Samples (8) GSM575753, GSM575790, GSM577075, GSM577076, GSM577077, GSM577078 
Series (1)
GSE23535 Performance of Immunochip 1.0 with hemolymph samples collected at 3 and 48 hours from Vibrio-challenged mussels

Data table header descriptions
ID
Array Row Array row position in the mussel Immunochip 1.0
Array Column Array column position in the mussel Immunochip 1.0
Spot Row Row oligoprobe position in array
Spot Column Column oligoprobe position in array
Oligo_ID Oligoprobe Identifier in Mytibase (http://mussel.cribi.unipd.it)
GB_ACC GenBank Accession Number
SPOT_ID
SEQUENCE Oligoprobe nucleotide sequence

Data table
ID Array Row Array Column Spot Row Spot Column Oligo_ID GB_ACC SPOT_ID SEQUENCE
1 1 1 1 1 Alignment Grid --control
2 1 1 1 2 Alignment Grid --control
3 1 1 1 3 Alignment Grid --control
4 1 1 2 1 Alignment Grid --control
5 1 1 2 2 MGO_00175 AJ516796 TGTTCCGTGGTCGTATGTCAATGAAGGAAGTAGATGAACAAATGTTGAACGTAC
6 1 1 2 3 MGO_02253 AJ624592 ATTGTGATTTTTGGCAGACGAATCTTCTTCCTGACGATGTTAGAAAAATGAAGGAC
7 1 1 2 4 MGO_00449 FL593837 TTTTATTATGGAAGGATTTAATGGTTTGTGGAAAGCTGATGAATTTACTACCCTTCA
8 1 1 2 5 MGO_01552 AJ516731 AGAGGTATATTTTGCATACAAGGATATGAATACATATGTGAACAAGAAAACAACAAC
9 1 1 2 6 MGO_01080 EH663389 AACACAGTAATGGACATCAATCATTGAATCACATTGGTTCTAATCTTCGATATA
10 1 1 2 7 MGO_04165 FL499517 AAGAAAGAGATAACGGAAGATTCAAATCAGGAAAAAGACTTTTGATTGGAGGAGGA
11 1 1 2 8 MGO_00475 EH663236 GGATTGTCTGTCAACTTATCATAAACGGTTAAAATGGAAATAATAAATATACATGAA
12 1 1 2 9 MGO_01570 AJ516766 TCAGAAGGAGGAGTTTAGTGTGTTAAAAGACTTAAATGATACATCATGTGTATTTCG
13 1 1 2 10 MGO_03930 FL499052 CTTGTACAGGATCCTCAGAGAACTTGTGTGTTTGTACACTGGATTATTCACCAG
14 1 1 2 11 MGO_05141 FL501220 ATTATCATTCTGTTGTCGGATATGGATTGGCAGTTGGGTCTAAAATTTTACGTGTG
15 1 1 2 12 MGO_00500 FL496549 CAGTAATGATTTTTGGGGAGGGTGGAAATGATTTCACAAGTACTTACTAATAGCTGT
16 1 1 2 13 MGO_01604 FL497632 TATTGTTGAAGAATTGTAACCCAGATGAGAAGGAAGAGATAATAGAACCTGTGTCTA
17 1 1 2 14 MGO_04329 FL499928 CGACCTTGATTCCGGTAATGTACGTGTTGGTATATTGTCATACAGTACAGCTGT
18 1 1 2 15 MGO_07024 FL490366 AAAGAATATGGTATCTAACATTTCAAGCTCACGACTCTCATGGTGATACTTTATGG
19 1 1 2 16 MGO_00509 FL594213 CTAAAAATGTCTCACTGTTTTCTTACTCATTTATATTATGACTGTGATAGGATGTTG
20 1 1 2 17 MGO_01640 AJ516897 ATTTGGTATAACTATATGCAATGATATAATGTATTGTTTCAAAACTGACGATGAAAC

Total number of rows: 10864

Table truncated, full table size 809 Kbytes.




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