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Platform GPL5622 Query DataSets for GPL5622
Status Public on Jul 20, 2007
Title SLA_PrV porcine DNA/cDNA microarray
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Sus scrofa
Manufacturer LREG, CRB_GADIE, INRA Jouy en Josas, France, F_78350
Manufacture protocol The SLA/PrV microarray, composed of cDNA and sub-cloned exons, is a dedicated array containing porcine and PrV probes. This microarray was constructed in the CRB-GADIE (Centre de Ressources Biologiques-Génomique des Animaux Domestiques et d'Intérêt Economique, LREG, INRA, Jouy-en Josas, France). The list of genes present in the human SLA orthologous region (6p21-p23) was drawn up using the human sequence draft (May 2004) on UCSC web site (http://genome.ucsc.edu/). Corresponding porcine cDNA clones were selected when they were available in the AGENAE library or in 2 American libraries MARC1PIG and MARC2PIG constructed in US by the United States Departement of Agriculture (USDA). When no porcine cDNA clone was found, exons were identified by comparison between ESTs and genomic DNA using ICCARE comparison mapping tool (http://genopole.toulouse.inra.fr/Iccare/). Primers were designed with Primer 3 (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi).PrV amplicons (80) targeting 70 genes an pig exons were amplified by PCR and subcloned (PGEMT easy plasmid, Promega and XXX). cDNA and sub-cloned exons were amplified by PCR (Taq PCR Master Mix Kit, Qiagen) with universal primers located in the vector (35 cycles:30 sec at 94°C, 30 sec at 60°C and 2 min at 70°C). After purification (Multiscreen-PCR plates, Millipore), PCR products were checked on 1% agarose gel, quantified (Fluoroscan), evaporated and pellets were resuspended in 13µl SSC3X. Forty six control spots were added on the slide (Lucidea Universal scorecard, Amersham Biosciences). Two identical arrays were spotted on slides (25x75 mm, UltraGAPS Coated Slides, Corning) with a 16 needles spotter (Microarraywriter Pro,Virtek). After spotting, slides were first treated with steam to homogenise spots hydratation. Then spotted DNA was denatured (5 sec at 100°C) and UV fixed (300 mJ). Slides were stored in dry atmosphere before use. All the SLA and immune clones spotted on the SLA/PrV slides were sequenced. Sequence homology was checked by multi-alignement (BLAST) against human and pig EST database (NCBI and VEGA). The SLA/PrV microarray probes were reannotated taking into account the most significant BLAST results and his final geneID file was used in the analysis.
Support Glass (25x75 mm, UltraGAPS Coated Slides, Corning)
Coating Aminosilane
 
Description Two identical networks per slide were spotted. A network contains 16 blocks with 12 rows and 12 columns for each block.
 
Contributor(s) Flori L, Rogel-Gaillard C, Hugot K, Chardon P
Submission date Jul 19, 2007
Last update date Jul 20, 2007
Contact name Laurence Flori
E-mail(s) laurence.flori@jouy.inra.fr
Organization name INRA
Department Génétique Animale
Lab LREG
Street address Domaine de Vilvert
City Jouy en Josas
ZIP/Postal code 78350
Country France
 
Samples (48) GSM215145, GSM215146, GSM215147, GSM215148, GSM215149, GSM215150 
Series (1)
GSE8676 PrV/PK15 kinetics_SLA/PrV slides

Data table header descriptions
ID
Block
X
Y
GeneName
GB_ACC GenBank Accession number
SPOT_ID

Data table
ID Block X Y GeneName GB_ACC SPOT_ID
scag0001.a.01 1 1 1 6642187.1.ss.5 BX665243
scag0001.e.01 1 2 1 Aminopeptidase N BX665286
scag0005.a.01 1 3 1 ASNS_CRIGR Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine- dependent asparagine synthetase). BX666565
scag0005.e.01 1 4 1 GRL1_MOUSE Gamma-aminobutyric acid receptor-associated protein-like 1 (GABA(A) receptor-associated protein-like 1) (Glandular epithelial cell protein 1) (GEC-1). BX666198
scag0009.a.01 1 5 1 COX3_PIG Cytochrome c oxidase polypeptide III (EC 1.9.3.1). BX666461
scag0009.e.01 1 6 1 C-X-C chemokine receptor type 6 BX665547
scaa0001.c.05 1 7 1 TRIM38 TRIM38
scaa0005.l.19 1 8 1 CCT7 (OldName:LOC221324) CCT7 (OldName:LOC221324)
scaa0024.i.14 1 9 1 GSTZ1 (OldName:TAP2) GSTZ1 (OldName:TAP2)
scac0044.d.21 1 10 1 HLA-DQB1 BX673913
xcbb0001.a.01 1 11 1 ORF1 ORF1
xcbb0001.e.01 1 12 1 UL13 UL13
scag0001.a.03 1 1 2 Heat shock protein HSP 9-alpha BX667427
scag0001.e.03 1 2 2 Putative HIF-prolyl hydroxylase PH-4 BX665289
scag0005.a.03 1 3 2 \N -- NO INFORMATION
scag0005.e.03 1 4 2 Amyloid beta A4 protein precursor BX666200
scag0009.a.03 1 5 2 Glutathione S-transferase Mu 5 BX666463
scag0009.e.03 1 6 2 Fibronectin BX665548
scaa0023.g.06 1 7 2 PRIM2A PRIM2A
scaa0024.i.14_1 1 8 2 GSTZ1 (OldName:TAP2) GSTZ1 (OldName:TAP2)

Total number of rows: 2304

Table truncated, full table size 126 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
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Supplementary data files not provided

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