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Platform GPL3649 Query DataSets for GPL3649
Status Public on Aug 01, 2006
Title PulseChip 1
Technology type spotted DNA/cDNA
Distribution non-commercial
Organisms Cicer arietinum; Lathyrus sativus; Lens culinaris
Manufacturer RMIT University, School of Applied Sciences, Bundoora AUSTRALIA
Manufacture protocol Coram TE and Pang ECK. 2006. Expression profiling of chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Published in Plant Biotechnology Journal.

A total of 715 ESTs, 41 RGA DNA sequences, and 12 controls were used in the construction of 768-feature microarrays according to minimum information about a microarray experiment guidelines (MIAME). Of the 715 ESTs, 516 were obtained from a previously synthesized and characterized EST collection constructed from cDNA of the ascochyta blight resistant ICC3996 chickpea genotype. Briefly, 1021 ESTs were generated from stem/leaf tissue of ICC3996 harvested after inoculation with A. rabiei spores, and assembled into 516 unigenes employed in the construction of this microarray. A single clone was selected to represent each contig. A further 43 chickpea cDNAs whose sequencing reactions had previously failed were also included in this microarray. The remaining 156 ESTs represent potential defence-related ESTs from a grasspea (Lathyrus sativus) cDNA library constructed from the Mycosphaerella pinodes resistant genotype ATC80878. Finally, the 41 RGA sequences were isolated from lentil (Lens culinaris) genotypes ILL6002 (A. lentis susceptible) and ILL7537 (A. lentis resistant). The 12 controls included negative, printing, and blank buffer controls. All samples were dried in 384-well plates before being resuspended in 10 µL 50% (v/v) dimethylsulphoxide:water at 250 ng/µL, and arrayed onto amino-silanized slides (Corning Incorporated Life Sciences, Acton, MA) using a BioRobotics® MicroGrid II Compact (Genomic Solutions, Ann Arbor, MI) with four Microspot 2500 pins (Genomic Solutions, Ann Arbor, MI). Blank buffer spots, digested vector and PCR primer were also incorporated as negative controls, as well as Cy5-10T as a printing control. Each element was deposited six times with a volume of approximately 6 nL and diameter of 200 µm. Slides were pre-hybridised by blocking in 5X SSC, 0.1% SDS, 25% Formamide, 1% BSA for 45 min at 42ºC, rinsed in distilled water and dried.
Support glass
Coating aminosilane
 
 
Contributor(s) Coram TE, Pang EC, Mantri NL, Mustafa BM
Submission date Apr 11, 2006
Last update date Nov 08, 2007
Contact name Tristan Coram
E-mail(s) tristan.coram@ars.usda.gov
Organization name USDA-ARS, NC State University
Street address 4118 Williams Hall, NC State University
City Raleigh
State/province NC
ZIP/Postal code 27695
Country USA
 
Samples (62) GSM105169, GSM105170, GSM105171, GSM105172, GSM105173, GSM105174 
Series (6)
GSE4660 Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei
GSE7416 Gene expression profiling of chickpea responses to drought stress
GSE7417 Gene expression profiling of chickpea responses to cold stress

Data table header descriptions
ID
GB_ACC GenBank Accession Number
Gene Name Putative functional gene identification
ORGANISM Source organism for each feature
MetaRow Array MetaRow
MetaColumn Array MetaColumn
Row Array Row
Column Array Column
Biosequence Type Type of array sequence
Reporter Usage Experimental or control use
Control Type Control type
SEQUENCE Primer sequences used for amplification if applicable
SPOT_ID spot identifier

Data table
ID GB_ACC Gene Name ORGANISM MetaRow MetaColumn Row Column Biosequence Type Reporter Usage Control Type SEQUENCE SPOT_ID
Blank1 1 2 1 9 Blank Control Negative NA --BLANK_negative control
Blank2 1 2 1 10 Blank Control Negative NA --BLANK_negative control
Blank3 1 4 1 9 Blank Control Negative NA --BLANK_negative control
Blank4 1 4 1 10 Blank Control Negative NA --BLANK_negative control
CA0009 Cicer arietinum (chickpea ICC3996) 1 2 7 12 cDNA clone Experimental NA NA --BAD READ
CA0011 NORMCON2 Cicer arietinum (chickpea ICC3996) 1 3 4 4 cDNA clone Control Normalisation NA CONTROL_Normalisation control 1
CA0014 EB085013 26S rRNA Cicer arietinum (chickpea ICC3996) 1 4 7 12 cDNA clone Experimental NA NA
CA0015 EB085014 Unknown Cicer arietinum (chickpea ICC3996) 1 2 7 13 cDNA clone Experimental NA NA
CA0018 NORMCON3 Cicer arietinum (chickpea ICC3996) 1 2 5 11 cDNA clone Control Normalisation NA CONTROL_Normalisation control 2
CA0020 NORMCON4 Cicer arietinum (chickpea ICC3996) 1 4 5 11 cDNA clone Control Normalisation NA CONTROL_Normalisation control 3
CA0021 Cicer arietinum (chickpea ICC3996) 1 4 7 13 cDNA clone Experimental NA NA --BAD READ
CA0030 Cicer arietinum (chickpea ICC3996) 1 2 7 14 cDNA clone Experimental NA NA --BAD READ
CA0032 Cicer arietinum (chickpea ICC3996) 1 4 7 14 cDNA clone Experimental NA NA --BAD READ
CA0036 Cicer arietinum (chickpea ICC3996) 1 1 6 1 cDNA clone Experimental NA NA --BAD READ
CA0043 DY475531 Unclear Cicer arietinum (chickpea ICC3996) 1 3 6 1 cDNA clone Experimental NA NA
CA0049 Cicer arietinum (chickpea ICC3996) 1 1 6 2 cDNA clone Experimental NA NA --BAD READ
CA0106 EB085015 Translational activator Cicer arietinum (chickpea ICC3996) 1 3 6 2 cDNA clone Experimental NA NA
CA0108 Cicer arietinum (chickpea ICC3996) 1 1 6 3 cDNA clone Experimental NA NA --BAD READ
CA0112 EB085065 18S rRNA Cicer arietinum (chickpea ICC3996) 1 1 6 10 cDNA clone Experimental NA NA
CA0178 EB085016 Unknown Cicer arietinum (chickpea ICC3996) 1 3 6 3 cDNA clone Experimental NA NA

Total number of rows: 768

Table truncated, full table size 85 Kbytes.




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

Supplementary file Size Download File type/resource
GPL3649_Full array layout.XLS.xls.gz 134.6 Kb (ftp)(http) XLS

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