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Platform GPL7151 Query DataSets for GPL7151
Status Public on Feb 01, 2009
Title SLA/Immune Response/NRSP8 Pig 70 mers Oligonucleotides 3.8K + 13.3K v1
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Sus scrofa
Manufacturer CRB GADIE
Manufacture protocol 1-1. Oligos from 13K set are arrayed by Operon in Genetix 384-well V-bottom plates. Each well contains 600 pmol of 70-mer oligo.
1-2. Resuspend oligos in water(20µM).
1-3. Incubate at room temperature during a night shaking plates to aid resuspension of DNA.
1-4. Deep freeze and defrost centrifuging plates at 1000 rpm for 16 minutes then 2000 rpm for 3 minutes.
1-5. Take 5 µl of oligos solution and put it in new Genetix polypropylene v-bottom plates (cat# X7022)
1-6. Add 5 µL of 1X Corning Printing Buffer to each well and mix.
2-1. Oligos from 3.8K SLA/Immune response set are arrayed by Operon in Genetix 384-well V-bottom plates. Each well contains 200 pmol of 70-mer oligo.
2-2. Resuspend oligos in water(20µM).
2-3. Incubate at room temperature during a night shaking plates to aid resuspension of DNA.
2-4. Deep freeze and defrost centrifuging plates at 1000 rpm for 16 minutes then 2000 rpm for 3 minutes.
2-5. Add 5 µL of 1X Corning Printing Buffer to each well and mix.
3-1. cDNA from Lucidea microarray Scorecard (GE Healthcare) are resuspended in water (100ng/µl).
3-2. Incubate at room temperature during a night shaking plates to aid resuspension of DNA.
3-3. Deep freeze and defrost centrifuging tubes at 1000 rpm for 16 minutes then 2000 rpm for 3 minutes.
3-4. Take 5 µl of solution and put it in new Genetix polypropylene v-bottom plates (cat# X7022). Each cDNA Lucidea scorecard are put 4 times.
3-5. Add 5 µL of 1X Corning Printing Buffer to each well and mix.
4. Centrifuge plates at 2000 rpm for 3 minutes.
5. Oligos are ready for spotting.
6. Spotting on glass slides (Corning, Ultragaps), with 48 Microspotting pins Stealth 3 on Chipwriter (Virtek), with control of humidity (45-50%).
7. Fixation of the oligos slides with UV (600 mJoules).
8. Storage the slides in a vacuum.
9. After the print run is completed, cover oligos plates with seals and deepfreeze them at -20°C in a protected environment.
Support glass
Coating aminosilane
 
Description The oligos set used for this microarray is a mix of the 13,3k generic set from Operon and a 3.8K SLA/Immune response specific set designed by Yu Gao (LREG-INRA) and synthetised by Operon.
 
Submission date Aug 08, 2008
Last update date Feb 01, 2009
Contact name Sylvain Marthey
E-mail(s) abridge@inra.fr
Organization name INRA
Department Animal Genetics
Lab Animal Genetics and Integrative Biology
Street address Domaine de Vilvert Bat 320
City Jouy-en-Josas
ZIP/Postal code 78352
Country France
 
Samples (276) GSM433321, GSM433322, GSM433323, GSM433324, GSM433325, GSM433326 
Series (4)
GSE17320 Transcriptome analysis of porcine PMBCs after stimulation by LPS or PMA/ionomycin using SLA-RI/NRSP8-13K chip
GSE25491 Transcriptomic and nuclear architecture of immune cells after LPS-activation
GSE45196 The peripheral blood transcriptome reflects variations in immunity traits in swine: toward identification of biomarkers

Data table header descriptions
ID
Block
Column
Row
GB_ACC
Accession
Description
SEQUENCE
SPOT_ID

Data table
ID Block Column Row GB_ACC Accession Description SEQUENCE SPOT_ID
SS00000707 1 1 1 TC183540 UP|ADML_PIG (P53366) ADM precursor [Contains: Adrenomedullin (AM); Proadrenomedullin N-20 terminal peptide (ProAM-N20) (ProAM N-terminal 20 peptide) (PAMP)], complete GCCCACAAACTGATTTCTGAAGGGGAATAACCCCAACAGGGCGCAAGCCTCACTATTACTTGAACTTTCC TC183540
SS00000701 1 2 1 GCGTTTCGGTTTCCGGCTTCAGAGCTCTCGTCTGGGATCCCGGTTTCGAGTCTAGAGGCTGTTTGCGGAC --UNKNOWN
SS00000683 1 3 1 TC187679 UP|FTCD_PIG (P53603) Formimidoyltransferase-cyclodeaminase (Formiminotransferase-cyclodeaminase) (FTCD) [Includes: Glutamate formimidoyltransferase (Glutamate formiminotransferase) (Glutamate formyltransferase); Formimidoyltetrahydrofolate cycl , complet TTCAAACCCAAGGAGCGGATTATCGAGTACCTGGTCCCCGAAGCTGGGCCTGAGCAGAGCCTGCTGCACA TC187679
SS00000677 1 4 1 TC183370 UP|Q8MJD6 (Q8MJD6) Odd homeobox 1 protein, complete TGGAAAACACTCGGGCTGGAAGACCGAAACTCCAGCCAGCAGAAAGTCAAGTAACTAAGGGGAAAAATTT TC183370
SS00000375 1 5 1 TC197501 homologue to UP|SORL_HUMAN (Q92673) Sortilin-related receptor precursor (Sorting protein-related receptor containing LDLR class A repeats) (SorLA) (SorLA-1) (Low-density lipoprotein receptor relative with 11 ligand-binding repeats) (LDLR relative with 11 CGTGTCTTACGACTACGGAAGATCATTCAAGAGAATCTCAGAGAAACTGAACTTCGGCACGGGGAACAGC TC197501
SS00000369 1 6 1 TC178449 similar to UP|Q8TC32 (Q8TC32) Serine/threonine kinase 36 (Fused homolog, Drosophila), partial (18%) AGGGTGATCTGATAAGGGACGTGGCTGGCTCAGAAATGTGGACTGTCCTTTGGCACCGCTTCGCCATGGC TC178449
SS00000351 1 7 1 TC170466 homologue to UP|ADAS_HUMAN (O00116) Alkyldihydroxyacetonephosphate synthase, peroxisomal precursor (Alkyl-DHAP synthase) (Alkylglycerone-phosphate synthase) , partial (69%) AACTTTTAGAGAGTGGATCGAAAATATCCTTGGAGTAAGTCTGGAGCATAAAACTACCTCTAAAGCATCC TC170466
SS00000345 1 8 1 TC171435 similar to UP|DAPT_HUMAN (O15228) Dihydroxyacetone phosphate acyltransferase (DHAP-AT) (DAP-AT) (Glycerone-phosphate O-acyltransferase) (Acyl-CoA:dihydroxyacetonephosphateacyltransferase) , partial (28%) TGTGAGATCCTCGATGAGATGAGCCACAAACTGCATCTGGGAGCCATTCGGTTTTTCGCCTTTGCCCTGA TC171435
SS00000327 1 9 1 CTGCTCGCAGTGTGCCACCTCGCCTCCCGCCGCTACCGAGGCAATGATTCATGTGAATACCTTCTCTCAA --UNKNOWN
SS00000321 1 10 1 GGTTCCTTCATTGTTGTGAACAGTCCCACCCACAGTTCTGGACTTCAGTGACCCCTTCAGCACAGAGGTG --UNKNOWN
SS00000303 1 11 1 TC181981 homologue to UP|TCPB_HUMAN (P78371) T-complex protein 1, beta subunit (TCP-1-beta) (CCT-beta), complete TGGTAAAGAGCACGTTGGGACCCAAGGGCATGGATAAAATTCTATTAAGCAGTGGACGAGATGCTTCTCT TC181981
SS00000297 1 12 1 TC163310 homologue to GB|AAC50423.1|1255188|HSU50733 dynamitin {Homo sapiens;} , complete CGGAGGAGCTGACGAGTACAAGTGTGGAGCACATCATTGTCAATCCCAATGCTGCCTATGACAAGTTCAA TC163310
SSNC000006 1 13 1 Randomized negative control ATACTTTGTTGACAGAGGAGCGCCCGGCCTCCCCGTGGAGGCCTTTGCTTATCGAAGTTCAAATCAGGGT --CONTROL: Negative
SS00004130 1 14 1 TC181280 UP|TBA6_MOUSE (P05216) Tubulin alpha-6 chain (Alpha-tubulin 6), partial (69%) ACAGTGCTGAGGGAGAAGATGAGGGTGAAGAGTATTAACCCGTCTGCTGCAGTTTTGCACTCTTGTGACT TC181280
SSNC000006.2 1 15 1 Randomized negative control ATACTTTGTTGACAGAGGAGCGCCCGGCCTCCCCGTGGAGGCCTTTGCTTATCGAAGTTCAAATCAGGGT --CONTROL: Negative
SS00004130.2 1 16 1 TC181280 UP|TBA6_MOUSE (P05216) Tubulin alpha-6 chain (Alpha-tubulin 6), partial (69%) ACAGTGCTGAGGGAGAAGATGAGGGTGAAGAGTATTAACCCGTCTGCTGCAGTTTTGCACTCTTGTGACT TC181280
SSNC000006.3 1 17 1 Randomized negative control ATACTTTGTTGACAGAGGAGCGCCCGGCCTCCCCGTGGAGGCCTTTGCTTATCGAAGTTCAAATCAGGGT --CONTROL: Negative
SS00004130.3 1 18 1 TC181280 UP|TBA6_MOUSE (P05216) Tubulin alpha-6 chain (Alpha-tubulin 6), partial (69%) ACAGTGCTGAGGGAGAAGATGAGGGTGAAGAGTATTAACCCGTCTGCTGCAGTTTTGCACTCTTGTGACT TC181280
SSNC000006.4 1 19 1 Randomized negative control ATACTTTGTTGACAGAGGAGCGCCCGGCCTCCCCGTGGAGGCCTTTGCTTATCGAAGTTCAAATCAGGGT --CONTROL: Negative
SS00004130.4 1 20 1 TC181280 UP|TBA6_MOUSE (P05216) Tubulin alpha-6 chain (Alpha-tubulin 6), partial (69%) ACAGTGCTGAGGGAGAAGATGAGGGTGAAGAGTATTAACCCGTCTGCTGCAGTTTTGCACTCTTGTGACT TC181280

Total number of rows: 19200

Table truncated, full table size 3019 Kbytes.




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