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Platform GPL9710 Query DataSets for GPL9710
Status Public on Jul 28, 2010
Title Operon Pig 14.4K genome microarray v1.0.2
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Sus scrofa
Manufacturer Operon
Manufacture protocol The Operon pig genome oligo set contains 10,665 70-mer probes with a hit to a known human, mouse, and pig gene transcript and some sequences containing a 3' EST. The pig genome oligo extension set contains 2,632 70-mer probes rpepresenting 2,632 gene sequences with at least one 3' EST. In total, 13,297 pig probes are included on the array (IDs start SS0). All probes were designed from The Institute of Genome Research (TIGR) Sus scrofa Gene Index (SsGI) version 5.0, released on October 1st 2002. All Transcript Consensus (TC) sequences and singleton expressed transcripts (ETs) were aligned using BLAST to known human, mouse, and pig genes. All TCs and singleton ETs with a more than 75% homology over at least 100 bases to a known human, mouse, or pig transcript and yielding a designed probe of less than or equal to 70% cross hybridization identity was included in the set. All probes were designed from the sense strand. They were also designed to have a Tm of 78°C +/- 5°C, be within 1,000 bases from the 3' end of the transcript, not have any contigous single base repeat of more than 8 bases in length, not have a potential hairpin structure with a stem length of more than 9 bases, and not have more than 20 contigous bases common to any other gene. All the component ESTs used to make the TCs were obtained from Genbank. All ESTs with the keyword 3', denoting a 3' EST, were marked and oligos designed in the same way. In addition to these pig probes, various negative controls are also included on the array. These include 10 sequences from the SpotReport Alien cDNA validation System from Stratagene (sequences designed to have no sequence homology to other genomes - IDs start Alien), 7 randomized probe sequences and 4 genes from the plant Arabidopsis thaliana (IDs start SSN), and 13 sequences from bacteria or viruses (from Affymetrix synthetic microarray sequences - IDs start NC). Probes were contact printed on glass aminosilane coated slides (Schott Nexterion) using a arraying robot and a 48 pin tool. Each subgrid on the array contains spots in a 24 row by 25 column grid. The top 12 rows in each subgrid are a repeat of the bottom 12.
 
 
Submission date Nov 20, 2009
Last update date Jul 28, 2010
Contact name James Michael Wilkinson
E-mail(s) jamiewilkinson@hotmail.com
Organization name University of Alberta
Department Agriculture, Food, and Nutritional Science
Street address Ag/For Building
City Edmonton
State/province Alberta
ZIP/Postal code T6G 2P5
Country Canada
 
Samples (89) GSM474373, GSM474374, GSM474375, GSM474376, GSM474377, GSM474378 
Series (2)
GSE19126 Comparison of Gene Expression in Lung of Pigs Exhibiting Different Susceptibilities to Glasser's Disease
GSE25854 Transcriptomics adaptation of porcine adipose- and bone marrow-derived stem cells during adipogenic and osteogenic differentiation

Data table header descriptions
ID
IDx
gene_id
description
top_hit_human_RefSeq
human_RefSeq_description
top_hit_mouse_RefSeq
Mouse_RefSeq_description
top_hit_pig_known_gene
top_hit_human_Ensembl
top_hit_mouse_Ensembl
SEQUENCE probe sequence
SPOT_ID
GB_ACC GenBank accession number

Data table
ID IDx gene_id description top_hit_human_RefSeq human_RefSeq_description top_hit_mouse_RefSeq Mouse_RefSeq_description top_hit_pig_known_gene top_hit_human_Ensembl top_hit_mouse_Ensembl SEQUENCE SPOT_ID GB_ACC
01: A-01 empty empty NONE NONE NONE NONE NONE NONE NONE NONE NONE --empty
01: A-02 empty empty NONE NONE NONE NONE NONE NONE NONE NONE NONE --empty
01: A-03 SS00000001 SS00000001 NONE NONE NM_006213 Homo sapiens phosphorylase kinase, gamma 1 (muscle) (PHKG1), mRNA NM_011079 Mus musculus phosphorylase kinase gamma 1 (Phkg1), mRNA AF091609 ENST00000297373 ENSMUST00000026617 GATTCCCATGGGATGGTGTCGCCAAGTCAATCTTCCCAGACCGTTTTACAACCCACGGTGTGCTTTAAAG --unknown
01: A-04 SS00000096 SS00000096 TC191359 homologue to GB|AAH09362.1|14424692|BC009362 SETDB1 protein {Homo sapiens;} , partial (32%) NM_012432 Homo sapiens SET domain, bifurcated 1 (SETDB1), mRNA NM_018877 Mus musculus SET domain, bifurcated 1 (Setdb1), mRNA NONE ENST00000271640 ENSMUST00000015841 TCATGGATGCCGTCAACAAGAAGAGCAGTTCCCAGGATCTTCACAAAGGAACCTTGAGTCAGATGACTGG SsGI: TC191359
01: A-05 SS00000002 SS00000002 NONE NONE NONE NONE NONE NONE NONE ENST00000269290 NONE CCCGCGGCGATGAAACAGTTGTAGCTGACTTGCTCGTAGAGCTTGTATATGTCCTGGGGGCCATTCTCAA --unknown
01: A-06 SS00000097 SS00000097 TC166903 UP|Q7YZQ6 (Q7YZQ6) Rab5 (Fragment), partial (5%) NM_012300 Homo sapiens F-box and WD-40 domain protein 11 (FBXW11), transcript variant 3, mRNA NM_134015 Mus musculus F-box and WD-40 domain protein 11 (Fbxw11), mRNA NONE ENST00000296933 ENSMUST00000076383 AAAGCAGCCTAACTCGTCAAGTACCGACATTTCTCACCTCCGAGTCCGGCCTCGACGTTGAGAAGGATAC SsGI: TC166903
01: A-07 SS00000003 SS00000003 TC180931 homologue to UP|CA13_HUMAN (P02461) Collagen alpha 1(III) chain precursor, partial (93%) NM_000090 Homo sapiens collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) (COL3A1), mRNA NM_009930 Mus musculus procollagen, type III, alpha 1 (Col3a1), mRNA AJ289758 ENST00000304636 ENSMUST00000041074 AGACACAGGACCCCCTGGTCAACAAGGATTACAAGGCTTGCCTGGAACCAGTGGTCCTCCAGGAGAAAAT SsGI: TC180931
01: A-08 SS00000098 SS00000098 TC174342 similar to UP|SDC1_CRIGR (P47951) Syndecan-1 precursor (SYND1), partial (36%) NM_002997 Homo sapiens syndecan 1 (SDC1), transcript variant 2, mRNA NM_011519 Mus musculus syndecan 1 (Sdc1), mRNA NONE ENST00000254351 ENSMUST00000020911 CATCGCGGGCGGCCTCGTGGGGCTTATCTTTGCCGTGTGCCTGGTGGGTTTCATGCTGTACCGGATGAAG SsGI: TC174342
01: A-09 SS00000004 SS00000004 TC180812 type I collagen alpha 1 chain [Sus scrofa] NM_000088 Homo sapiens collagen, type I, alpha 1 (COL1A1), mRNA NM_007742 Mus musculus procollagen, type I, alpha 1 (Col1a1), mRNA AJ289757 ENST00000225964 ENSMUST00000001547 CCCAGAAGAACTGGTACATCAGCAAGAACCCCAAGGACAAGAGGCACGTCTGGTACGGCGAGAGCATGAC SsGI: TC180812
01: A-10 SS00000099 SS00000099 NONE NONE NM_001235 Homo sapiens serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1) (SERPINH1), mRNA NM_009825 Mus musculus serine (or cysteine) proteinase inhibitor, clade H, member 1 (Serpinh1), mRNA NONE ENST00000341643 NONE CATGGTGACCGTTCTATACGTGGGTGTACTATGATGACGGACAGGCTCTACACTATATGAGACGAGAGGA --unknown
01: A-11 SS00000005 SS00000005 TC180807 homologue to UP|SPRC_BOVIN (P13213) SPARC precursor (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement membrane protein BM-40), complete NM_003118 Homo sapiens secreted protein, acidic, cysteine-rich (osteonectin) (SPARC), mRNA NM_009242 Mus musculus secreted acidic cysteine rich glycoprotein (Sparc), mRNA NONE ENST00000231061 ENSMUST00000018737 CGAGTTTGAGAAGGTATGCAGCAATGACAACAAGACCTTTGACTCTTCCTGCCACTTCTTTGCCACCAAG SsGI: TC180807
01: A-12 SS00000100 SS00000100 TC161978 homologue to UP|TCPH_HUMAN (Q99832) T-complex protein 1, eta subunit (TCP-1-eta) (CCT-eta) (HIV-1 Nef interacting protein), complete NM_006429 Homo sapiens chaperonin containing TCP1, subunit 7 (eta) (CCT7), mRNA NM_007638 Mus musculus chaperonin subunit 7 (eta) (Cct7), mRNA NONE ENST00000258091 ENSMUST00000032078 TGAAACCCTATGTGGAAGAAGGTTTGCACCCACAGATCATCATCCGAGCTTTCCGCACTGCCACTCAGCT SsGI: TC161978
01: A-13 SS00000006 SS00000006 NONE NONE NM_000938 Homo sapiens polymerase (RNA) II (DNA directed) polypeptide B, 140kDa (POLR2B), mRNA NM_153798 Mus musculus polymerase (RNA) II (DNA directed) polypeptide B (Polr2b), mRNA NONE ENST00000314595 ENSMUST00000031167 TAAATTAGGTCTAGCAGAAAGAGTGAAATACCGAAGCCAGTTAAGAGAGGGAACCACCAGAGGCCAAGGT --unknown
01: A-14 SS00000101 SS00000101 TC189011 homologue to UP|Q99KF3 (Q99KF3) Nxn protein, partial (62%) NM_022463 Homo sapiens nucleoredoxin (NXN), mRNA NM_008750 Mus musculus nucleoredoxin (Nxn), mRNA NONE ENST00000336868 ENSMUST00000021204 AGGAACCGGCTGCTGGTGATCCGCGATGACCCGGAAGGTTTGGAATTCCCTTGGGGACCTAAGCCCTTCA SsGI: TC189011
01: A-15 SS00000007 SS00000007 NONE NONE NM_001005 Homo sapiens ribosomal protein S3 (RPS3), mRNA NM_012052 Mus musculus ribosomal protein S3 (Rps3), mRNA NONE ENST00000278572 ENSMUST00000032998 GTGAGGAGTAGGTGTCATGTGTAAGAAAGGTGTCTCCCTGTACAGTCAGAGGGGAATAATGCCGACTTCT --unknown
01: A-16 SS00000102 SS00000102 TC181904 homologue to UP|SYQ_HUMAN (P47897) Glutaminyl-tRNA synthetase (Glutamine--tRNA ligase) (GlnRS) , complete NM_005051 Homo sapiens glutaminyl-tRNA synthetase (QARS), mRNA NM_133794 Mus musculus glutaminyl-tRNA synthetase (Qars), mRNA NONE ENST00000306125 ENSMUST00000006838 AGATACGTACCCGGTTCCCACCAGAACCCAACGGAATCCTGCACATTGGACATGCCAAAGCCATCAATTT SsGI: TC181904
01: A-17 SS00000008 SS00000008 TC162822 GB|CAA61857.1|3218320|HSDAP5 death associated protein 5 {Homo sapiens;} , partial (64%) NM_001418 Homo sapiens eukaryotic translation initiation factor 4 gamma, 2 (EIF4G2), mRNA NM_013507 Mus musculus eukaryotic translation initiation factor 4, gamma 2 (Eif4g2), mRNA NONE ENST00000339995 ENSMUST00000005750 CCTTCATGATCATGTTGATCTACAAGTCAGTGCTCTCTATGCTCTTCAGGTGCACTGCTACAACAGCAAC SsGI: TC162822
01: A-18 SS00000103 SS00000103 TC192867 UP|Q96SB3 (Q96SB3) Neurabin II protein, partial (22%) NM_032595 Homo sapiens protein phosphatase 1, regulatory subunit 9B, spinophilin (PPP1R9B), mRNA NM_172261 Mus musculus protein phosphatase 1, regulatory subunit 9B (Ppp1r9b), mRNA NONE ENST00000316878 ENSMUST00000038696 AAGCTAGTGCACAAGTTCAAGGAGCTCCAGATCAAGCATGCTGTTGACTGAGGCAGAGATCCAGCAGCTG SsGI: TC192867
01: A-19 SS00000009 SS00000009 TC182915 homologue to GB|AAF34356.1|6979206|AF153085 phosphoprotein pp75 {Homo sapiens;} , partial (13%) NM_015470 Homo sapiens RAB11 family interacting protein 5 (class I) (RAB11FIP5), mRNA NM_177466 Mus musculus RAB11 family interacting protein 5 (class I) (Rab11fip5), transcript variant 2, mRNA NONE ENST00000258098 ENSMUST00000060837 CTGTTCTCGTTGCCTGTCCAGAAGCCAAAAACTCTGTGCTGCTGCAGGGTTTGAACTTTCGAAAACCAAT SsGI: TC182915
01: A-20 SS00000104 SS00000104 TC192936 homologue to UP|Q6FHL6 (Q6FHL6) PTK9 protein, partial (52%) NM_002822 Homo sapiens PTK9 protein tyrosine kinase 9 (PTK9), transcript variant 1, mRNA NM_008971 Mus musculus protein tyrosine kinase 9 (Ptk9), mRNA NONE ENST00000325127 ENSMUST00000023087 TTTGCTGTCGCAGTCTTCTCCTGCCCCACTGACTGCAGCTGAGGAAGAATTACGACAGATTAAAATTAAT SsGI: TC192936

Total number of rows: 14353

Table truncated, full table size 4871 Kbytes.




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