NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL5171 Query DataSets for GPL5171
Status Public on Mar 15, 2008
Title Pork Quality Operon 70-mer oligo array
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Sus scrofa
Manufacturer Oligos:Qiagen-Operon, Printed by: National Engineering Center for Biochip(Shanghai,China)
Manufacture protocol The 152 probes from the Pig Genome Oligo Set and Extension V1.0 (OMAD Release: 04/13/04) representing 140 key genes involved in porcine muscle growth and adipose metabolism. The Qiagen 70-mer oligos designed from TIGR Tentative Consensus cDNA sequences and minimized cross-hybridization. The probes are Tm normalized to 78ºC (±5ºC) and have a 5' amino linker. The probes were printed on GAPS II Slides(Corning)coated with amino-silane by OmniGrid 100(GeneMachine),and post-processed according to the manufacturer's protocol.
Support glass
Coating aminosilane
 
 
Web link http://www.operon.com/arrays/oligosets_pig.php
Contributor(s) Li M, Li X, Zhu L, Guo Y, Chen L, Li Q, Shuai S, Jiang A, Yang G, Tang G, Jiang Y
Submission date May 17, 2007
Last update date Mar 15, 2008
Contact name Mingzhou Li
E-mail(s) mingzhou.li@163.com
Phone 86-835-2886000
Organization name Sichuan Agricultural University
Department College of Animal Science and Technology
Lab Institute of Animal Genetics and Breeding
Street address No.46 Xinkang Road
City Ya'an
State/province Sichuan
ZIP/Postal code 625014
Country China
 
Samples (38) GSM190566, GSM190568, GSM190569, GSM190570, GSM190571, GSM190572 
Series (4)
GSE7856 Comparison between Backfat Tissue of Fat Type Pig and Lean Type Pig, among developmental phases
GSE7857 Comparison between longissimus dorsi muscle tissue of Fat and Lean Type Pig, among developmental phases
GSE7858 Comparison among longissimus dorsi muscle of 3 pig breeds, among developmental phases of Tibetan Pig

Data table header descriptions
ID
Oligo_ID Oligo tracking IDs from Qiagen-Operon (Designer of the 70-mer porcine oligos)
Metarow Meta row of slide
Metacol Meta column of slide
Subrow Row of block
Subcol column of block
SEQUENCE The 70-mer oligo sequences spotted on the array.
SPOT_ID 'Positive Control', oligos were designed from housekeeping genes; 'Negative Control', oligos designed to not hybridize to Pig genome.
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.

Data table
ID Oligo_ID Metarow Metacol Subrow Subcol SEQUENCE SPOT_ID Description TIGR_TC_ID
1 SS00000714 1 1 1 1 TGCCAAAGCCTTAGACAAGCGCCAAGCCCATCTTTGTGTGCTTGCATCCAACTGTGATGAGCCAATGTAT -- Positive Control UP|Q6PDW1 (Q6PDW1) Rps12 protein, complete TC163257
2 SS00010186 1 1 1 2 TCAGCAAGGACTGGTCTTTCTACCTTCTGGTCCACACTGAGTTCACTCCTAACGCTGTGGATCAGTATAG -- Positive Control UP|B2MG_PIG (Q07717) Beta-2-microglobulin precursor (Lactollin), complete TC162655
3 SS00000626 1 1 1 3 CAGCACATTTTGCGAGTACTCAACACCAACATCGATGGGCGGCGGAAAATTGCCTTTGCTATCACTGCGA -- Positive Control UP|RS18_HUMAN (P62269) 40S ribosomal protein S18 (Ke-3) (Ke3), complete TC181715
4 SS00000654 1 1 1 4 TGCAGCGTTTCATTAAGATAGACGGCAAGGTCCGCACTGATATAACCTACCCCGCTGGTTTTATGGATGT -- Positive Control UP|RS4X_CERAE (Q76N24) 40S ribosomal protein S4, X isoform, complete TC162859
5 SS00000721 1 1 1 5 CTGTTGACTGCATGTATCAGTCCTCTAGGAGTTAGGATGAACCCCGTTGATGGGAGTAGCTATCCTTAGG -- Positive Control GB|AAC48718.1|1945447|SSU94395 90-kDa heat shock protein {Sus scrofa;} , complete TC181434
6 SS00001180 1 1 1 6 GTGACTTCAACAGTGACACTCACTCTTCTACCTTTGATGCTGGGGCTGGCATTGCCCTCAACGACCACTT -- Positive Control UP|G3P_PIG (P00355) Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) , complete TC162668
7 SSNC000001 1 1 1 7 CACACATAACTTCCGATCATAACGAACCTAGGCGAGCCGACTAGTTAGCTAGCGATCTGGCTGCCGTGCA -- Negative Control Randomized negative control
8 SSNC000002 1 1 1 8 GCCTTAAATCAGTACGCTGACAAATCATCCATCGAGGAGTTTTGCGTTGGCCCTGACGGCCGTACTTGGC -- Negative Control Randomized negative control
9 SSNC000005 1 1 1 9 ACTCTGCAGAACGCGTCGTCTTACACTACCCATTGGACTCAGTATTAATTCCATCGTATGCAGCCTCAGC -- Negative Control Randomized negative control
10 SSNC000009 1 1 2 1 ACGCTGGTGCGGGTCGTATGGGTGGTACTACTCAGTACACTGTCAACAACCAGATGGTTAACGCAACACT -- Negative Control Arabidopsis thaliana mRNA for rubisco activase
11 SSNC000010 1 1 2 2 GCTTCTTCCCACGATTACTCCATCGTTGGATACTCCCCCGAGGATTTGGAATCTCATGACAAACTCATAG -- Negative Control Arabidopsis thaliana papain-type cysteine endopeptidase XCP2
12 SSNC000011 1 1 2 3 AGCTGCTGAATCTTCTACTGGTACATGGACAACTGTGTGGACCGATGGGCTTACCAGCCTTGATCGTTAC -- Negative Control Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, chloroplast gene encoding chloroplast protein
13 SS00009742 1 1 2 4 CAACCTGGAGACGCAGCATAAGGTCCTGGAGCTCACGGCCGAGAACGAGCGGCTCCAGAAGAAGGTGGAG TIGR TC181252 CCAAT/enhancer binding protein beta [Sus scrofa] TC181252
14 SS00001123 1 1 2 5 AAATGCCAGTATTGTCGTTTCCACAAGTGCCTCTCGGCCGGGATGTCCCATAATGCAATTCGATTTGGGC TIGR TC173390 UP|Q9N135 (Q9N135) Peroxisome proliferator activated receptor alpha (Fragment), complete TC173390
15 SS00000944 1 1 2 6 CTCCCTCCTCAGCTCCCCTCTCTCTCATCTCTTTGCTCTTTCTTTTCCTTCCTCTCTCAGCCTCGCTTTC TIGR TC188129 UP|Q866Q2 (Q866Q2) Peroxisome proliferator-activated receptor delta, complete TC188129
16 SS00009666 1 1 2 7 CTGGTGGGCAGCAATGGGACCATTCTGACCACAATGCCTGTGATGATGGGGCAAGAGAAAGTGCCCATTA TIGR TC173040 sterol regulatory element binding protein-2 [Sus scrofa] TC173040
17 SS00010137 1 1 2 8 TTCAGTATCTGACACCCAGCACAGGCCTGCTGAGGATAACTGATTCAAGTCAGAAGAGTGAAATGCAGAC TIGR TC182134 UP|Q6Q781 (Q6Q781) Calpastatin, complete TC182134
18 SS00010143 1 1 2 9 CCATATACAAACAGTTCGATGTTGACCGTTCAGGGACCATTGGCAGCAGTGAACTCCCAGGGGCCTTTGA TIGR TC181761 UP|CSS1_PIG (P04574) Calpain small subunit 1 (CSS1) (Calcium-dependent protease small subunit 1) (Calcium-dependent protease small subunit) (CDPS) (Calpain regulatory subunit) (Calcium-activated neutral proteinase small subunit) (CANP small subunit) , com TC181761
19 SS00001174 1 1 3 1 TCTCTCATCTTGTCATGCCCAGCCTGGCCCTTTAGTTAAGGAATGGAAGGAGGGAGAACAACTGTCCCTC TIGR TC167354 UP|CAN3_PIG (P43368) Calpain 3 (Calpain L3) (Calpain p94) (Calcium-activated neutral proteinase 3) (CANP 3) (Muscle-specific calcium-activated neutral protease 3) (nCL-1) , complete TC167354
20 SS00001156 1 1 3 2 CCAGCGCCACACGGACATGCCCAAGGCTCAGAAGGAAGTACATTTGAAGAACACAAGTAGAGGGAGTTCA TIGR TC185593 UP|IGF1_PIG (P16545) Insulin-like growth factor I precursor (IGF-I) (Somatomedin), complete TC185593

Total number of rows: 656

Table truncated, full table size 127 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.