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Platform GPL13457 Query DataSets for GPL13457
Status Public on Apr 30, 2011
Title NCSU_chicken_JS3 (359 oligos)
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Gallus gallus
Manufacturer NCSU animal genomics laboratory
Manufacture protocol 1.70-mer oligos synthetized by Operon Biothechnologies Inc. Oligos were resuspended in Tris buffer; 250 µM of each oligo was added to one well of one of two 384-well plates (A and B) and dried (312 oligos in plate A and 47 oligos in plate B).
2. Oligos were resuspended in Universal Spotting Solution (Corning, Inc)
3. Seal plates with Corning seals.
4. Shake plate at mid speed on plate vortexer for 1 minute.
5. Remove seal and place plate on appropriate place on VersArray ChipWriter array printer.
6. Place UltraGaps Amino-Silane Coated Slides on appropriate place on array printer
7. Run pin clean-up steps 5 times before start printing (using 1 pin)
8. Start printing run
9. Turn-off printer once run is completed
10. Take plate from printer, seal it with Corning seal and store it at -20 oC
11. Let slides dry on printer for 24h
12. Crosslink slides on UV over set to 6000 x 100 µJ/cm2, store slides on secator
 
Description Each well was spotted 3 times (side-by-side) in the same grid, and grids were replicated 4 times on each slide; therefore, each gene was spotted a total of 12 times on the array. From the 480 wells printed (resulting in 5760 spots), 359 had an actual oligo (312 from plate A and 47 from plate B) and 121 had only spotting solution. These spots were annotated as NA (empty wells) and were not included in the statistical analysis resulting in output files containing 4308 spots (359 oligos as 12 replicates).
 
Contributor(s) Baurhoo BS, de Oliveira JE, Druyan S, Ashwell CM
Submission date Apr 29, 2011
Last update date May 05, 2011
Contact name Bushansingh Shyam Baurhoo
E-mail(s) baurhoo.bushansingh@mail.mcgill.ca
Phone 514 659 8276
Organization name McGill University
Department Animal Science
Street address 21111, Lakeshore Road
City Ste Anne de Bellevue
State/province Quebec
ZIP/Postal code H9X 3V9
Country Canada
 
Samples (68) GSM717528, GSM717529, GSM717530, GSM717531, GSM717532, GSM717533 
Series (1)
GSE28959 Differential expression of innate immune and metabolic genes in LPS-challenged chickens

Data table header descriptions
ID
Well_ID
SPOT Location of printed oligonucleotide sequence on array
Gene_Symbol Gene symbols
Gene Gene names
ORF Gene ID available at Entrez Gene (NCBI)
SEQUENCE 70 mer unique oligo sequence for the gene
SPOT_ID spot identifier

Data table
ID Well_ID SPOT Gene_Symbol Gene ORF SEQUENCE SPOT_ID
1 A_a1 380 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
2 A_a1 400 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
3 A_a1 420 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
4 A_a1 1820 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
5 A_a1 1840 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
6 A_a1 1860 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
7 A_a1 3260 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
8 A_a1 3280 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
9 A_a1 3300 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
10 A_a1 4700 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
11 A_a1 4720 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
12 A_a1 4740 ANKRD1 Ankyrin repeat domain 1 (cardiac muscle) 378926 ATTTGTGTCACCTGAGAACGCTTTTTTTTTCCCCATAAGAACCATGGCCTGTCTCTGCTCGCCGTCCT
13 A_a10 1340 DIO2 Deiodinase Type 2 373903 AACGCAAGCAATTTTGAAGGAGCCGGGGTCTTGCAGTGACTTTGCATAGAATGCAGTCGAGTGTGGCATT
14 A_a10 1360 DIO2 Deiodinase Type 2 373903 AACGCAAGCAATTTTGAAGGAGCCGGGGTCTTGCAGTGACTTTGCATAGAATGCAGTCGAGTGTGGCATT
15 A_a10 1380 DIO2 Deiodinase Type 2 373903 AACGCAAGCAATTTTGAAGGAGCCGGGGTCTTGCAGTGACTTTGCATAGAATGCAGTCGAGTGTGGCATT
16 A_a10 2780 DIO2 Deiodinase Type 2 373903 AACGCAAGCAATTTTGAAGGAGCCGGGGTCTTGCAGTGACTTTGCATAGAATGCAGTCGAGTGTGGCATT
17 A_a10 2800 DIO2 Deiodinase Type 2 373903 AACGCAAGCAATTTTGAAGGAGCCGGGGTCTTGCAGTGACTTTGCATAGAATGCAGTCGAGTGTGGCATT
18 A_a10 2820 DIO2 Deiodinase Type 2 373903 AACGCAAGCAATTTTGAAGGAGCCGGGGTCTTGCAGTGACTTTGCATAGAATGCAGTCGAGTGTGGCATT
19 A_a10 4220 DIO2 Deiodinase Type 2 373903 AACGCAAGCAATTTTGAAGGAGCCGGGGTCTTGCAGTGACTTTGCATAGAATGCAGTCGAGTGTGGCATT
20 A_a10 4240 DIO2 Deiodinase Type 2 373903 AACGCAAGCAATTTTGAAGGAGCCGGGGTCTTGCAGTGACTTTGCATAGAATGCAGTCGAGTGTGGCATT

Total number of rows: 4308

Table truncated, full table size 546 Kbytes.




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