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Platform GPL16188 Query DataSets for GPL16188
Status Public on Apr 16, 2013
Title Operon Array-Ready 29K Oligo Sets for the Pig Genome Version 1.0 and the Pig Genome Oligo Extension Set Version 1.0
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Sus scrofa
Manufacturer Operon
Manufacture protocol Oligonucleotides were printed in duplicate on epoxide slides by operon. Operon probes are designed from The TIGR Gene Index Database SsGI Release 5.0 released 10/1/02. The Oligo set contains 10,665 70mer probes representing 10,665 Sus scrofa gene sequences with a hit to a known human, mouse, or pig transcript and some sequences containing a 3' expressed sequence tag. The Pig Genome Oligo Extension Set Version 1.0 contains 2,632 70mer probes representing 2632 Sus scrofa gene sequences with at least one 3' EST.
 
Description Zhao SH, Recknor J, Lunney JK, Nettleton D, Kuhar D, Orley S, Tuggle CK: Validation of a first-generation long-oligonucleotide microarray for transcriptional profiling in the pig.Zhao SH, Recknor J, Lunney JK, Nettleton D, Kuhar D, Orley S, Tuggle CK., Genomics. 2005 Nov;86(5):618-25.
 
Citation(s) 16216716
Submission date Oct 16, 2012
Last update date Mar 25, 2013
Contact name Marcel Hulst
E-mail(s) marcel.hulst@wur.nl
URL http://www.livestockresearch.wur.nl
Organization name Animal Sciences Group
Department Livestock research
Lab Animal Breeding and Genomic Centre
Street address Edelhertweg 15
City Lelystad
State/province Flevoland
ZIP/Postal code 8219 PH
Country Netherlands
 
Samples (18) GSM1020370, GSM1020371, GSM1020372, GSM1020373, GSM1020374, GSM1020375 
Series (1)
GSE41630 Transcription networks responsible for early regulation of Salmonella-induced inflammation in the jejunum of pigs.

Data table header descriptions
ID unique identifier
BLOCK spot position: patch
COLUMN spot position: vertical column
ROW spot position: horizontal row
OLIGO_ID Oligo tracking IDs from Qiagen-Operon (Designer of the 70-mer porcine oligos)
SEQUENCE The 70-mer oligo sequences spotted on the array
GENE DESCRIPTION Annotation of the TIGR TC consensus sequence from which the 70-mer oligos on the array were designed
TIGR_TC_ID TIGR TC consensus sequence accession numbers, oligos were designed from these TCs
SPOT_ID

Data table
ID BLOCK COLUMN ROW OLIGO_ID SEQUENCE GENE DESCRIPTION TIGR_TC_ID SPOT_ID
1 1 1 1 SS00000297 CGGAGGAGCTGACGAGTACAAGTGTGGAGCACATCATTGTCAATCCCAATGCTGCCTATGACAAGTTCAA homologue to GB|AAC50423.1|1255188|HSU50733 dynamitin {Homo sapiens;} , complete TC163310 TIGR: TC163310
2 1 1 2 SS00001443 CCCACTAACAGTGACTAAAATAACCCCAGGCTGTTGACTGCATTCACATCGCCCTCTGTGCCTGATGTCA similar to UP|MTN3_HUMAN (O15232) Matrilin-3 precursor, partial (4%) TC164202 TIGR: TC164202
3 1 1 3 SS00002601 ACAGTCCAGGTTTTGTAGAATATGTGATGGACCGGTCCGTAGAGCATGACAAAGCTTCAAAGGATGCCAA PSMD5 subunit [Sus scrofa] TC165981 TIGR: TC165981
4 1 1 4 SS00003747 AACATGAGGCCCCCAAACAACAGCAGTCCAGTACAAGAGGATACAGAAAATGCATCTTGTGAGCTTTGTG homologue to GB|AAT06732.1|46946999|AY598321 L2 {Homo sapiens;} , partial (56%) TC171496 TIGR: TC171496
5 1 1 5 SS00004905 CTGTATGATACCAGCATCCTGTACTGCTACGAGGCATCCCTTCCACATCAGATCAAAGACATCTTAAAGC homologue to UP|RRP4_HUMAN (Q13868) Exosome complex exonuclease RRP4 (Ribosomal RNA processing protein 4) (Exosome component 2) , partial (21%) TC186060 TIGR: TC186060
6 1 1 6 SS00006051 TTGTGAACGCTCCATACAAGCGAGGCTTCTACTGCGGAGATGACTCCATCCGGTACCCCTACCGTCCAGA homologue to UP|LPP2_HUMAN (O43688) Lipid phosphate phosphohydrolase 2 (Phosphatidic acid phosphatase 2c) (Phosphatidate phosphohydrolase type 2c) (PAP2c) (PAP-2c) (PAP2-gamma) (PAP2-G) , partial (67%) TC164865 TIGR: TC164865
7 1 1 7 SS00007209 AGAACCTTACTCATACACTTGTTGGGGGGGATGTACAGTGCATAACCCCAAGCTGTGGAAAGGACACTTT homologue to UP|Q6JUT2 (Q6JUT2) TIRAP3b long form, partial (47%) TC164868 TIGR: TC164868
8 1 1 8 SS00008355 GCACACACTGCATGTTCAGGGCACTCAAACACTGCCTCTTAATGTATTTTCCACGGCCTCGTCCCGACGA similar to UP|Q86VE0 (Q86VE0) LOC339344 protein (Fragment), partial (6%) TC184507 TIGR: TC184507
9 1 1 9 SS00009797 CTTCCACGACACCTATGAAACCAACACACCCAGCTGCTGTGCCAAGGAGCTGGCAGAAATGAAGCGGGAA UP|IRK5_PIG (O02670) G protein-activated inward rectifier potassium channel 4 (GIRK4) (Potassium channel, inwardly rectifying, subfamily J, member 5) (Inward rectifier K+ channel Kir3.4) (Heart KATP channel) (KATP-1) (Cardiac inward rectifier) (CIR), complete TC176089 TIGR: TC176089
10 1 1 10 not applicable 29: D-13 empty not applicable --empty
11 1 1 11 SS00011800 GTAGCGCTAGAATTTCCTACCCTATTGTCCAAGCTGCTTTCTCCCAGAAAGGGGCTAGCAATGGTGACAT similar to UP|O50155 (O50155) Proton-translocating ATPase, b subunit, partial (8%) TC171132 TIGR: TC171132
12 1 1 12 SS00013242 CCCACCATGATGGAATCAGGTCGTCTTTGAGAATGGAAATTGACTCTGCAGACTTTGGTTCTGTATTTGA unknown TC167794 TIGR: TC167794
13 1 1 13 SS00000297 CGGAGGAGCTGACGAGTACAAGTGTGGAGCACATCATTGTCAATCCCAATGCTGCCTATGACAAGTTCAA homologue to GB|AAC50423.1|1255188|HSU50733 dynamitin {Homo sapiens;} , complete TC163310 TIGR: TC163310
14 1 1 14 SS00001443 CCCACTAACAGTGACTAAAATAACCCCAGGCTGTTGACTGCATTCACATCGCCCTCTGTGCCTGATGTCA similar to UP|MTN3_HUMAN (O15232) Matrilin-3 precursor, partial (4%) TC164202 TIGR: TC164202
15 1 1 15 SS00002601 ACAGTCCAGGTTTTGTAGAATATGTGATGGACCGGTCCGTAGAGCATGACAAAGCTTCAAAGGATGCCAA PSMD5 subunit [Sus scrofa] TC165981 TIGR: TC165981
16 1 1 16 SS00003747 AACATGAGGCCCCCAAACAACAGCAGTCCAGTACAAGAGGATACAGAAAATGCATCTTGTGAGCTTTGTG homologue to GB|AAT06732.1|46946999|AY598321 L2 {Homo sapiens;} , partial (56%) TC171496 TIGR: TC171496
17 1 1 17 SS00004905 CTGTATGATACCAGCATCCTGTACTGCTACGAGGCATCCCTTCCACATCAGATCAAAGACATCTTAAAGC homologue to UP|RRP4_HUMAN (Q13868) Exosome complex exonuclease RRP4 (Ribosomal RNA processing protein 4) (Exosome component 2) , partial (21%) TC186060 TIGR: TC186060
18 1 1 18 SS00006051 TTGTGAACGCTCCATACAAGCGAGGCTTCTACTGCGGAGATGACTCCATCCGGTACCCCTACCGTCCAGA homologue to UP|LPP2_HUMAN (O43688) Lipid phosphate phosphohydrolase 2 (Phosphatidic acid phosphatase 2c) (Phosphatidate phosphohydrolase type 2c) (PAP2c) (PAP-2c) (PAP2-gamma) (PAP2-G) , partial (67%) TC164865 TIGR: TC164865
19 1 1 19 SS00007209 AGAACCTTACTCATACACTTGTTGGGGGGGATGTACAGTGCATAACCCCAAGCTGTGGAAAGGACACTTT homologue to UP|Q6JUT2 (Q6JUT2) TIRAP3b long form, partial (47%) TC164868 TIGR: TC164868
20 1 1 20 SS00008355 GCACACACTGCATGTTCAGGGCACTCAAACACTGCCTCTTAATGTATTTTCCACGGCCTCGTCCCGACGA similar to UP|Q86VE0 (Q86VE0) LOC339344 protein (Fragment), partial (6%) TC184507 TIGR: TC184507

Total number of rows: 28800

Table truncated, full table size 5470 Kbytes.




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