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Status
Public on Feb 01, 2010
Title
Turkey skeletal muscle long oligonucleotide (TSKMLO) microarray
Technology type
spotted oligonucleotide
Distribution
non-commercial
Organism
Meleagris gallopavo Manufacturer
Oligonucleotide design and synthesis: Invitrogen (Carlsbad, CA); Array printing: Michigan State University Research Technology Support Facility (East Lansing, MI)
Manufacture protocol
Three skeletal muscle cDNA libraries from the developmental stages 18-day embryo, 1-day post-hatch chick, and 16-week market age bird were constructed and sequenced as in Reed et al. (2008). Additional sequences for genes important in regulation of muscle growth, development, and extracellular matrix function were added. Because alternative splicing has been identified as a potential mechanism in the differential regulation of the Ca2+ channel ryanodine receptor (RYR), possibly leading to downstream defects in postmortem meat quality (Chiang et al. 2004; Chiang et al. 2007), oligos were also designed to represent five different alternatively spliced products of RYR. In total, 5809 70-mer oligonucleotides were commercially designed (Invitrogen, Carlsbad, CA). A unique set of control probes were designed for thirty randomly chosen genes with the stipulation that the gene be greater than 1500 bases in length. These controls consisted of: one scrambled sequence control, three “distance” controls that included oligos designed within 500, 501-1000, and 1001-1500 bases from the 3’ of the sequence, and six “mismatch” controls including 3, 5, 10, 15, 20, or 25 mismatched bases, totaling 300 control probes.
Web link
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.2010.02085.x/pdf Contributor(s)
Sporer KR , Chiang W , Tempelman RJ , Ernst CW , Reed KM , Velleman SG , Strasburg GM Citation(s)
20528844 Submission date
Dec 11, 2009
Last update date
Jan 25, 2011
Contact name
Kelly R Sporer
E-mail(s)
buckhamk@msu.edu Phone
517-355-8474
Fax
517-432-0753
Organization name
Michigan State University
Department
Food Science and Human Nutrition
Lab
Muscle Biology and Genetics Research
Street address
3365 Anthony Hall
City
East Lansing
State/province
MI
ZIP/Postal code
48824
Country
USA
Samples (166)
GSM484748 , GSM484749 , GSM484750 , GSM484751 , GSM486551 , GSM486552
GSM486553 ,
GSM486554 ,
GSM486555 ,
GSM486558 ,
GSM486559 ,
GSM486560 ,
GSM486561 ,
GSM486562 ,
GSM486715 ,
GSM486716 ,
GSM486717 ,
GSM486718 ,
GSM486719 ,
GSM486720 ,
GSM486721 ,
GSM486722 ,
GSM486723 ,
GSM486724 ,
GSM486725 ,
GSM486726 ,
GSM486727 ,
GSM486728 ,
GSM486729 ,
GSM486730 ,
GSM486731 ,
GSM486732 ,
GSM486733 ,
GSM486734 ,
GSM486985 ,
GSM486986 ,
GSM486987 ,
GSM486988 ,
GSM486989 ,
GSM486990 ,
GSM486991 ,
GSM486992 ,
GSM486993 ,
GSM486994 ,
GSM487032 ,
GSM487033 ,
GSM487035 ,
GSM487072 ,
GSM487174 ,
GSM487175 ,
GSM487176 ,
GSM487177 ,
GSM487178 ,
GSM487179 ,
GSM487180 ,
GSM487181 ,
GSM487182 ,
GSM487183 ,
GSM487184 ,
GSM487238 ,
GSM487239 ,
GSM487240 ,
GSM487241 ,
GSM487242 ,
GSM487243 ,
GSM487244 ,
GSM487245 ,
GSM487246 ,
GSM487247 ,
GSM487248 ,
GSM487249 ,
GSM487250 ,
GSM487251 ,
GSM487252 ,
GSM573135 ,
GSM573136 ,
GSM573137 ,
GSM573138 ,
GSM573139 ,
GSM573140 ,
GSM573141 ,
GSM573142 ,
GSM573143 ,
GSM573144 ,
GSM573145 ,
GSM573146 ,
GSM573147 ,
GSM573148 ,
GSM573149 ,
GSM573150 ,
GSM573151 ,
GSM573152 ,
GSM573153 ,
GSM573154 ,
GSM573155 ,
GSM573156 ,
GSM573157 ,
GSM573158 ,
GSM573159 ,
GSM573160 ,
GSM573161 ,
GSM573162 ,
GSM573163 ,
GSM573164 ,
GSM573165 ,
GSM573166 ,
GSM573167 ,
GSM573168 ,
GSM671077 ,
GSM671078 ,
GSM671079 ,
GSM671080 ,
GSM873168 ,
GSM873169 ,
GSM873170 ,
GSM873171 ,
GSM873172 ,
GSM873173 ,
GSM873174 ,
GSM873175 ,
GSM873176 ,
GSM873177 ,
GSM873178 ,
GSM873179 ,
GSM873180 ,
GSM873181 ,
GSM873182 ,
GSM873183 ,
GSM889644 ,
GSM889645 ,
GSM889646 ,
GSM889647 ,
GSM889648 ,
GSM889649 ,
GSM889650 ,
GSM889651 ,
GSM889705 ,
GSM889707 ,
GSM889709 ,
GSM889711 ,
GSM889712 ,
GSM889714 ,
GSM889716 ,
GSM889718 ,
GSM889742 ,
GSM889743 ,
GSM889744 ,
GSM889745 ,
GSM889746 ,
GSM889747 ,
GSM889748 ,
GSM889749 ,
GSM889750 ,
GSM889751 ,
GSM889752 ,
GSM889753 ,
GSM889754 ,
GSM889755 ,
GSM889756 ,
GSM889757 ,
GSM898214 ,
GSM898215 ,
GSM898216 ,
GSM898217 ,
GSM898218 ,
GSM898219 Series (10)
GSE19452 TSKMLO microarray validation experiment
GSE19531 Analysis of the turkey skeletal muscle transcriptome through development within a genetic line (Experiment 1)
GSE19538 Analysis of the turkey skeletal muscle transcriptome between genetic lines within a developmental stage (Experiment 2)
GSE19585 Analysis of the turkey skeletal muscle transcriptome through development and between genetic lines
GSE23354 Differential Expression of Genes Characterizing Muscle Fiber Phenotype in Turkeys
GSE27147 Differential cardiac gene expression in genetically selected turkeys
GSE35660 Transcriptional profiling of turkey muscle satellite cells transfected with DAP-siRNA during proliferation and differentiation
GSE36362 Transcriptional profiling of turkey muscle satellite cells transfected with MGP-siRNA during proliferation and differentiation
GSE36365 Transcriptional profiling of turkey muscle satellite cells transfected with versican-siRNA during proliferation and differentiation
GSE36660 Differential expression of skeletal muscle genes between normal and pale, soft and exudative (PSE) turkey meat.
Data table header descriptions ID Block Block number of 48 blocks of oligos spotted on array
Row Row number of 16 rows of oligos spotted in each block
Column Column number of 16 columns of oligos spotted in each block
Oligo_ID Unique oligonucleotide identifier
SEQUENCE Oligonucleotide sequence
GB_ACC NCBI GenBank Accession Number
Best_Match_Accession Accession of Best_Match
Best_Match_Description SPOT_ID
Data table ID Block Row Column Oligo_ID SEQUENCE GB_ACC Best_Match_Accession Best_Match_Description SPOT_ID 1
1
1
1
alpha-RYR:12640-13455:j2
AGGGGACCCCGATCCTGAAGAGGAAGATCGGGGAGGATGGGAAGGAGGTGGTGGAGGAACCGCAGAAGGA
X95266.1
G.gallus mRNA for ryanodine receptor type 1
alpha-RYR:12640-13455:j2
2
1
1
2
CaMKIIB
ATGAGTACGCTGCCAAGATCATCAACACCAAGAAGCTCTCAGCCAGAGACCACCAGAAACTGGAGAGGGA
ES554297.1
TO1008B01SP6 TO1 Tribolium castaneum cDNA, mRNA sequence.
CaMKIIB
3
1
1
3
Contig[0194]
AAGTTGGGACAGACATCCTGGAGGAGGAGATCACCAAGTTTGAGGACTATGTGCAAAGTGTTGACATTGC
EL783943.1 Q4_Reed_1DPH_cDNA_04_L12_188.F Meleagris gallopavo 1DPH Meleagris gallopavo cDNA 5', mRNA sequence.
4
1
1
4
Contig[0233]
AAGTGAAGGATCTGCTCAGCTTAACTCAGTTCTTCGGCTTCCACACGGAGACCTTCTCGCTGGCTGTCAA
EH294080.1 Q1_Reed_1DPH_02_03_E03_037.F 1d_posthatch Meleagris gallopavo cDNA 5', mRNA sequence.
5
1
1
5
Contig[0486]
CTGTCTTGTATGAGTGCTGTCCTGGCTATATGAAGATGGATGGTATGAGAGGATGTCCTGCAGTTGCTCC
EH294251.1 Q2_Reed_1DPH_02_01_40H05.F 1d_posthatch Meleagris gallopavo cDNA 5', mRNA sequence.
6
1
1
6
Contig[0503]
TGCCAGAGGATGGCGCAGTTCGATGCCAAGAAGTTTGCTGAGAACCAAGCGAAGAAGGAGGGCCCGAAAA
EH293212.1 Q3_Reed_18d_tembryo_06_N23_366.F 14d_emb Meleagris gallopavo cDNA 5', mRNA sequence.
7
1
1
7
Contig[0663]
TGGAGCTGCAGAGAAAATAGAGAGAACGGTTCAAATTGAGGCTTCCACAGTAGAGATAGAGGAGCGGGGG
EH294431.1 Q4_Reed_1DPH_02_01_84D11.F 1d_posthatch Meleagris gallopavo cDNA 5', mRNA sequence.
8
1
1
8
Contig[0677]
CCTTCATCATGGATGGCAATCGCCGTTATGCCCAGAAGTGTCACGTGGAGAGGCAACAAGGACATTCACA
EH286212.1 Q3_Reed_1DPH_cDNA_03_J11_170.F 1d_posthatch Meleagris gallopavo cDNA 5', mRNA sequence.
9
1
1
9
Contig[0886]
GACGTGAAGTACGAACCTGAATGCAACCTGAAAGGTCCAAGCAGATGAGCTTTGTGACATCCTGTGCCAG
EH287559.1 Q4_Reed_1DPH_cDNA_05_B12_178.F 1d_posthatch Meleagris gallopavo cDNA 5', mRNA sequence.
10
1
1
10
Contig[0923]
AGAGAAGAAATCTAAGCGGCACGATAAGGCTCGGAAGAGGAAAGCTCAGACAGATGAAAGCGAGCAGTCG
EH288328.1 Q4_Reed_1DPH_cDNA_10_D24_372.F 1d_posthatch Meleagris gallopavo cDNA 5', mRNA sequence.
11
1
1
11
Contig[1123]
GAGATATCGCCCTGCTGAAAACCTACGGCCAGAGCACATACTCCAGGCAGATCAAGCAAGTAGAAGATGA
EH290944.1 Q4_Reed_16wkturkeymuscle_05_H10_152.F 16_week Meleagris gallopavo cDNA 5', mRNA sequence.
12
1
1
12
Contig[1222]
CTGTGACTGGCAGAAAGGAACAGTGTCCCTGAAGCCCACTGCTGTTCTGCACTGATCATCTTCCAGCCAG
EH286108.1 Q2_Reed_1DPH_cDNA_07_O08_127.F 1d_posthatch Meleagris gallopavo cDNA 5', mRNA sequence.
13
1
1
13
Contig[1588]
TGGCAGAAATGCCTCTGCTTGTTGACTAACTGCTTGCTGCTTGCTGCCAGGGTTGTAATGGATGGTGAGG
EH287794.1 Q4_Reed_1DPH_cDNA_07_P02_032.F 1d_posthatch Meleagris gallopavo cDNA 5', mRNA sequence.
14
1
1
14
Contig[1634]
CAGCTCTGCCAAACACAGAGAGAACACTGTAAGCCAAGAGAGGCCGGAGAAGATGGATGCTTTTTCCTCT
EH292867.1 Q3_Reed_18d_tembryo_02_D11_164.F 14d_emb Meleagris gallopavo cDNA 5', mRNA sequence.
15
1
1
15
Contig[2156]
GTATTACTCCCTGAAAGAATCTACCACCAGTGAGCAGAGTGCTAGGATGACTGCTATGGACAATGCAAGC
EH286155.1 Q3_Reed_1DPH_cDNA_02_P03_048.F 1d_posthatch Meleagris gallopavo cDNA 5', mRNA sequence.
16
1
1
16
Contig[2196]
CTGAGCTAGCGTGTCTCGTGTTTTGATGGGTAGGAGTGAGATCAGTCAGCAAAGTGACCTCTAGATGTGG
Contig[2196]
17
1
2
1
Contig[2561]
GTAAGAGAAAGGGTACAGCCAACGCTCGTATGCCAGAGAAGGTGACCTGGATGAGGAGGATGCGAATTCT
EH292934.1 Q3_Reed_18d_tembryo_07_D05_068.F 14d_emb Meleagris gallopavo cDNA 5', mRNA sequence.
18
1
2
2
Contig[2578]
ACTGCAGAAGTTGGGGACTACAGTAGGAAACTTCGGAAACACGCGGCAGAACTCGAGGAACGCGATCTGA
EH293290.1 Q4_Reed_18d_tembryo_02_B02_018.F 14d_emb Meleagris gallopavo cDNA 5', mRNA sequence.
19
1
2
3
Contig[2681]
CTCAGCACGTGTTCTTAATGTCCAGTGATTTTACCCAAGTTGCAAAAGCAAAATACAAATACTTCCTTTC
EH290283.1 Q3_Reed_16wkturkeymuscle_06_N15_238.F_0417 16_week Meleagris gallopavo cDNA 5', mRNA sequence.
20
1
2
4
Contig[2695]
AAGGGTGACAGCCAAAACGACGCCTGGATCTTCACACTGGCGCTGCTGTTGTCCAGCACCCTGGTGTACA
EH289647.1 Q2_Reed_16wkturkeymuscle_08_A16_241.F 16_week Meleagris gallopavo cDNA 5', mRNA sequence.
12288 2396 Kbytes .Supplementary data files not provided
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