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Platform GPL3800 Query DataSets for GPL3800
Status Public on May 26, 2006
Title population genetic approach to host patheogen response
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Homo sapiens
Manufacturer University of New Mexico Experimental Biology Laboratory
Manufacture protocol Oligonucleotide printing, microarray slide preparation and processing :Oligonucleotide libraries are printed on poly L Lysine coated microscope slides which are blocked prior to hybridization. Prior to printing, the microscope slides (Gold Seal, VWR, So. Plainfield, NJ) are cleaned with 2.5 M NaOH in 61% ethanol, washed thoroughly, and then coated with 0.01% poly l lysine (Sigma, St. Louis, MO) in filtered 10% phosphate buffered saline without calcium or magnesium (Hyclone, Logan, UT). After coating, excess poly l lysine is rinsed off and the slides are vacuum dried and stored at least 2 weeks prior to printing. The mouse ver 1.1 library of 70mer oligonucleotides (Operon, Alameda, CA) is resuspended at 40uM in 3xSSC in 384 well v bottom plates (Genetix, Beaverton, OR) prior to printing 100 slides on an OmniGrid Microarray printer (GeneMachines, San Carlos, CA). In brief, the printing conditions are 60% humidity, 16 Majer pins (Majer Precision Engineering, Tempe, AZ), 24 column by 22 row subarrays, 8448 features per array including controls, duplicate arrays per slide, 0 millisecond print time, and 22 384 well plates per print run. Between each sample, pins are cleaned with two loops of 3 second sonication, 2 second washing and 4 second drying per loop. Printed controls include 70mer oligonucleotides specific for constitutively expressed housekeeping genes (e.g. actin, 28s rRNA), 3xSSC printing buffer, blanks, murine genomic DNA, and B. subtilis gene pcr products (American Type Culture Collection, Rockville MD). After printing, the microarray slides are rehydrated, snap dried at 105oC, UV crosslinked at 65 mjoules (Stratalinker, Stratagene, LaJolla, CA) and blocked with 43mM sodium borate (Fisher, Fair Lawn, NJ) and 157mM succinic anhydride (Aldrich, Milwaukee, WI) in 1-methyl 2-pyrolidinone (Aldrich, Milwaukee, WI).
Support glass
Coating polysine
Contributor(s) Lyons CR, Rushton JJ
Submission date May 24, 2006
Last update date Jan 18, 2013
Contact name John Joseph Rushton
Phone 505-272-0738
Fax 505-272-4160
Organization name University of New Mexico, School of Medicine
Department Internal Medicine
Lab CRF 317
Street address MSC10 5550, 1 University of New Mexico
City Albuquerque
State/province NM
ZIP/Postal code 87131-0001
Country USA

Data table header descriptions
gene_id Unige feature identifier
transcript_count number of transcripts identified by the array feature
representative_transcript_id Genebank Reference number of for the trancript used for the sequence of the feature
HUGO Human genome organization clasification number
GB_ACC the ensemble genebank refence sequence for the feature
GB_ACC the EMBl reference number of the sequence
description name and description of the gene being detected

Data table
ID gene_id transcript_count representative_transcript_id HUGO GB_ACC GB_ACC description SPOT_ID
28s rRNA-1 28s rRNA -- 28s rRNA
28s rRNA-2 28s rRNA -- 28s rRNA
28s rRNA-3 28s rRNA -- 28s rRNA
28s rRNA-4 28s rRNA -- 28s rRNA
28s rRNA-5 28s rRNA -- 28s rRNA
28s rRNA-6 28s rRNA -- 28s rRNA
28s rRNA-7 28s rRNA -- 28s rRNA
28s rRNA-8 28s rRNA -- 28s rRNA
28s rRNA-9 28s rRNA -- 28s rRNA
28s rRNA-10 28s rRNA -- 28s rRNA
28s rRNA-11 28s rRNA -- 28s rRNA
28s rRNA-12 28s rRNA -- 28s rRNA
Blank-1 Blank -- Blank
Blank-2 Blank -- Blank
Blank-3 Blank -- Blank
Blank-4 Blank -- Blank
Blank-5 Blank -- Blank
Blank-6 Blank -- Blank
Blank-7 Blank -- Blank
Blank-8 Blank -- Blank

Total number of rows: 18432

Table truncated, full table size 1638 Kbytes.

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided

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