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Platform GPL3594 Query DataSets for GPL3594
Status Public on May 23, 2006
Title DIAS_PIG_27K2_v2
Technology type mixed spotted oligonucleotide/cDNA
Distribution non-commercial
Organism Sus scrofa
Manufacturer Danish Institute of Agricultural Sciences
Manufacture protocol The DIAS_PIG_27K2_v2 array consists of 27.648 features: 5.375 PCR products amplified from cDNA clones, 985 control features and 552 oligonucleotides spotted as quadruplicates. The array consists of 4 x 12 sub arrays each of 24 x 24 spots. The four replicated spots were spotted pair wise on different locations on the slide. Practically, the 6.912 elements were first spotted twice in 2 x 12 sub arrays (sub array-column 3 and 4). The source plates were then rotated 180 ° and the final 2 x 12 sub arrays (sub array-column 1 and 2) were spotted.
The cDNA clones used as template were selected from the cDNA libraries generated in the Sino-Danish Pig Genome Sequencing Consortium (Gorodkin et al.: Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 ESTs. Genome Biol 2007, 8:R45). The cDNA clones were selected by blasting the human sequences of genes of interest for similarity (P ≤ 10-8) to members of the porcine EST selection at DIAS. Furthermore, a number of clones were selected from lung, liver and muscle Longissimus dorsii cDNA libraries to represent major clusters of EST sequences.
The control features consists of dilution series of selected clones and oligonucleotides, genomic DNA from pig and salmon, sheared pig and salmon genomic DNA, ds cDNA from pig lung and muscle, different porcine C0t DNA fractions and blanks.
The 552 oligonucleotides (70-mer) were designed from the sequence of p450 related genes using the SEPON software (Hornshøj et al, “SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target Tm algorithm for reducing cross-hybridization in microarray gene expression experiments”, Bioinformatics. 2004 Feb 12;20(3):428-9).
The arrays were spotted on UltraGAPS slides (Corning Incorporated) at 20 C/55 % RH using an SDDC-2 MicroArrayer (BioRad) with 24 SMP3 stealth pins (Telechem International) with DNA resuspended in Micro Spotting Solution (Telechem International). Slides were dried and UV cross-linked (300 mJ) and stored in a vacuum desiccator until use.
Support glass
Coating aminosilane
 
 
Contributor(s) Bendixen C, Horn P, Hedegaard J, Conley LN, Hornshøj H, Panitz F
Submission date Mar 27, 2006
Last update date Apr 30, 2007
Contact name Jakob Hedegaard
E-mail(s) [email protected]
Phone (+45)89991363
Organization name Aarhus University, Faculty of Agricultural Sciences
Department Department of Genetics and Biotechnology
Lab Molecular Genetics and System Biology
Street address PO-box 50
City Tjele
ZIP/Postal code DK-8830
Country Denmark
 
Samples (6) GSM102063, GSM102064, GSM102071, GSM102074, GSM102075, GSM102076
Series (1)
GSE4577 Early pig response to experimental infection with Actinobacillus pleuropneomuniae

Data table header descriptions
ID
BLOCK
METACOLUMN
METAROW
COLUMN
ROW
REPORTER_ID Internal ID
REPLICA
REPORTER_TYPE
CONTROL_DESCRIPTION

Data table
ID BLOCK METACOLUMN METAROW COLUMN ROW REPORTER_ID REPLICA REPORTER_TYPE CONTROL_DESCRIPTION
100108.4 1 1 1 1 1 100108 4 cDNA NA
100108.3 1 1 1 2 1 100108 3 cDNA NA
100120.4 1 1 1 3 1 100120 4 cDNA NA
100120.3 1 1 1 4 1 100120 3 cDNA NA
100156.4 1 1 1 5 1 100156 4 cDNA NA
100156.3 1 1 1 6 1 100156 3 cDNA NA
100168.4 1 1 1 7 1 100168 4 cDNA NA
100168.3 1 1 1 8 1 100168 3 cDNA NA
100204.4 1 1 1 9 1 100204 4 cDNA NA
100204.3 1 1 1 10 1 100204 3 cDNA NA
100216.4 1 1 1 11 1 100216 4 cDNA NA
100216.3 1 1 1 12 1 100216 3 cDNA NA
100252.4 1 1 1 13 1 100252 4 cDNA NA
100252.3 1 1 1 14 1 100252 3 cDNA NA
100264.4 1 1 1 15 1 100264 4 cDNA NA
100264.3 1 1 1 16 1 100264 3 cDNA NA
100300.4 1 1 1 17 1 100300 4 cDNA NA
100300.3 1 1 1 18 1 100300 3 cDNA NA
100312.4 1 1 1 19 1 100312 4 cDNA NA
100312.3 1 1 1 20 1 100312 3 cDNA NA

Total number of rows: 27648

Table truncated, full table size 1101 Kbytes.




Download family Format
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Supplementary data files not provided

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