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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
GSM190573 ,
GSM190574 ,
GSM190575 ,
GSM190576 ,
GSM190577 ,
GSM190578 ,
GSM190579 ,
GSM190580 ,
GSM190581 ,
GSM190582 ,
GSM190583 ,
GSM190584 ,
GSM190585 ,
GSM190586 ,
GSM190587 ,
GSM190588 ,
GSM190589 ,
GSM190590 ,
GSM190591 ,
GSM190592 ,
GSM190593 ,
GSM190594 ,
GSM190595 ,
GSM190596 ,
GSM190597 ,
GSM190598 ,
GSM190599 ,
GSM190608 ,
GSM190609 ,
GSM190610 ,
GSM190612 ,
GSM190613
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
GSE7901
Swine Profiling of longissimus dorsi muscle and backfat
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 .
Supplementary data files not provided