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Platform GPL5755 Query DataSets for GPL5755
Status Public on May 19, 2011
Title Eucalyptus Array #1
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Eucalyptus nitens
Manufacturer Ensis Genetics/CSIRO Plant Industry
Manufacture protocol A cDNA library of genes expressed in differentiating xylem tissue from a vertical stem of E. grandis was constructed using the Stratagene lambda ZAP®II pre-digested vector kit (Stratagene, La Jolla, CA) with poly (A)+mRNA isolated by methods described previously (Southerton et al., 1998). The primary library was amplified before pBluescript phagemids were mass excised using the ExAssit/SOLR system (Stratagene, La Jolla, CA). Randomly picked phagemid colonies were cultured in a 96-well plate and the inserts amplified by PCR directly using forward, 5'-GTAAAACGACGGCCAGTG- 3' and reverse, 5'-GGAAACAGCTATGACCATG- 3' primers. The 100 ?l PCR reaction mixture contained 10 ?l of 10X PCR (-Mg2+) buffer, 2 ?l of 10 mM dNTP mixture, 5 ?l of primer mix (10 ?M each), 77.5 ?l of MilliQ water, 0.5 ?l of Taq DNA polymerase (5U ?l-1, LifeTechnologies, Rockville, MD) and 2 ?l supernatant 1 from overnight culture. Reactions were amplified on a 9600 GeneAmp PCR System (Perkin-Elmer, Foster City, CA) using the following PCR amplification programme: 3 min denaturation at 95 °C, 34 cycles of 30 s at 94°C, 30 s at 45°C and 2.5 min at 72°C, followed by a 7 min extension at 72°C. The PCR products were purified using the TIGR's filtration protocol (Hegde et al., 2000). After washing twice with 100 ?l of MilliQ water, 16 ?l of 3 X SSC was added to each well and shaken vigorously for 10 minutes on a shaker to resuspend the DNA. Approximately 4,900 cDNAs were printed onto Superaldehyde glass slides (TeleChem, Sunnydale, CA) using a Bio-Rad (Hercules, CA) VersArray Chipwriter Pro with SMP 3 stealth microspotting quill pins (TeleChem, Sunnydale, CA). Each cDNA was spotted twice by different pins on a different area of the same slide. Glass slides were processed according to the TeleChem protocols. Cy3-and Cy5-labeled (Amersham Pharmacia) cDNA probes were generated using the two-step labelling method described by Schenk et al. (2000). Application of the probe to microarray slides, hybridization, and subsequent washes of the slides were performed according to Schenk et al. (2000). For each tree, slides were hybridized with probes synthesized from vertical xylem and one or other of upper or lower branch xylem.
 
Description Random Eucalyptus cDNA
 
Web link http://www.pi.csiro.au/
Contributor(s) Southerton S, Wilson I
Submission date Aug 19, 2007
Last update date May 19, 2011
Contact name Andrew Spriggs
E-mail(s) andrew.spriggs@csiro.au
Phone 612-6246-5193
Organization name CSIRO Plant Industry
Department Bioinformatics Group
Street address GPO Box 1600
City Canberra
State/province ACT
ZIP/Postal code 2601
Country Australia
 
Samples (8) GSM219011, GSM219012, GSM219013, GSM219014, GSM219015, GSM219016 
Series (1)
GSE8816 EucalyptWood

Data table header descriptions
ID Unique Identifier for each feature
BLOCK Block within array (Synonymous with TIP ID)
COLUMN Column within array
ROW Row within array
CLONE ID
CLONE_LIB Clone Library
GB_ACC Genbank EST ID
GENE_FUNCTION Descriptive gene function, from NCBI Genbank accession or donor supplied
SPOT_ID Spot identifier

Data table
ID BLOCK COLUMN ROW CLONE ID CLONE_LIB GB_ACC GENE_FUNCTION SPOT_ID
SP0000439409 1 1 1 p71a7 Simon Southerton No Desc --UNKNOWN
SP0000438557 1 1 2 p65a7 Simon Southerton EW688215 No Desc GB_EST: EW688215
SP0000437701 1 1 3 p61a7 Simon Southerton No Desc --UNKNOWN
SP0000436849 1 1 4 p56a7 Simon Southerton No Desc --UNKNOWN
SP0000435995 1 1 5 p51a7 Simon Southerton No Desc --UNKNOWN
SP0000435141 1 1 6 p47a7 Simon Southerton No Desc --UNKNOWN
SP0000434291 1 1 7 p38a7 Simon Southerton No Desc --UNKNOWN
SP0000433435 1 1 8 p33a7 Simon Southerton No Desc --UNKNOWN
SP0000432583 1 1 9 p26a7 Simon Southerton No Desc --UNKNOWN
SP0000431729 1 1 10 p17a7 Simon Southerton No Desc --UNKNOWN
SP0000440859 1 1 11 p10a7 Simon Southerton No Desc --UNKNOWN
SP0000437841 1 1 12 p6a7 Simon Southerton No Desc --UNKNOWN
SP0000440691 1 1 13 p1a7 Simon Southerton No Desc --UNKNOWN
SP0000439410 1 1 14 p71a7 Simon Southerton No Desc --UNKNOWN
SP0000438558 1 1 15 p65a7 Simon Southerton EW688215 No Desc GB_EST: EW688215
SP0000437702 1 1 16 p61a7 Simon Southerton No Desc --UNKNOWN
SP0000436850 1 1 17 p56a7 Simon Southerton No Desc --UNKNOWN
SP0000435996 1 1 18 p51a7 Simon Southerton No Desc --UNKNOWN
SP0000435142 1 1 19 p47a7 Simon Southerton No Desc --UNKNOWN
SP0000434292 1 1 20 p38a7 Simon Southerton No Desc --UNKNOWN

Total number of rows: 9984

Table truncated, full table size 625 Kbytes.




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