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Platform GPL15067 Query DataSets for GPL15067
Status Public on Aug 07, 2012
Title UKM Lates calcarifer liver and spleen cDNA array
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Lates calcarifer
Manufacturer Universiti Kebangsaan Malaysia
Manufacture protocol Using the GeneTac™G3 (Genomic Solutions™, USA) arrayer, we fabricated the in-house Asian seabass (Lates calacrifer) cDNA microarray slide, comprising 1920 probes sourced from in-house Lates calcarifer spleen and liver cDNA libraries. Putative functions encoded by these probes include immunity, stress response, metabolism, transport, transcription and translation. Negative controls, such as oligonucleotide (A)50 and several Saccharomyces cerevisiae and Escherichia coli genes, as well as positive controls, such as a serial dilution of L. calcarifer genomic DNA and pooled cDNA, were also included. PCR amplification of the clones was carried out using a pair of M13 universal primers (Forward 5’-GTAAAACGACGGCCAG-3’, Reverse 5’-GTCATAGCTGTTTCCTG-3’) under the following conditions: initial denaturation at 95oC for 2 min, followed by 30 cycles of 95oC for 30 sec, 52 oC for 30 sec and 72 oC for 2 min, and a final extension step at 72 oC for 10 min. All the amplicons were checked with agarose gel electrophoresis and subsequently purified using Montage® PCRµ96 Plate (MilliPore, USA). The amplicon was resuspended in DMSO with the final concentration of probes ranging from 150-250 μg/mL. The probes were spotted twice onto aminosilane-coated glass slides (Corning, USA). The array consists of spots arranged in 4 x 8 grids. There are 32 grids in 4 columns (meta-columns) and 8 rows (meta-rows). Each of the grids contained 11 x 11 spots generating 121 spots per grid. Each fabricated slide contained a total of 3872 spots including 32 GeneTac™G3 arrayer prefix empty spots. Each spotted slide was left overnight in the arrayer. Subsequently, the slide was crosslinked at 300 mJ of ultraviolet (UV) irradiation with HoeferTM UVC 500 Crosslinker (Amersham Biosciences, UK) and stored in humidity and light-controlled conditions until use. Quality of the slide produced was assessed by a hybridization check with a random nanomer from the SpotCheckTM Slide QC kit (Genetix, USA).
Support glass
Coating aminosilane
Submission date Dec 27, 2011
Last update date Dec 27, 2011
Contact name Abdul Munir Abdul Murad
Organization name Universiti Kebangsaan Malaysia
Department Faculty of Science & Technology
Lab School of Bioscience & BioTechnology
Street address Jalan Universiti
City Bangi
State/province Selangor
ZIP/Postal code 43600
Country Malaysia
Samples (24) GSM854453, GSM854454, GSM854455, GSM854456, GSM854457, GSM854458 
Series (1)
GSE34745 Transcriptome Analysis of the Lates calcarifer Immune Response Towards Cryptocaryon irritans Infection

Data table header descriptions
DESCRIPTION Functional description of the gene

Data table
1 Pool cDNA P168
2 Poly A 50pM
3 insignicant match LSE02B06
4 immunoglobulin light chain precursor LSE02C11
5 unnamed protein product LSE09E03
6 selenoprotein P, LSE09E10
8 insignicant match LSE11G06
9 insignicant match LSE13F08
10 insignicant match LSE13G11
11 Genomic DNA G300
15 cytochrome c oxidase subunit III LSE23A09
16 cytochrome c oxidase subunit II LSE23B06
17 cathepsin D LSE24G01
18 NADH dehydrogenase subunit 2 LSE24G08
19 coatomer protein complex subunit beta 1 LSE26F01
20 insignicant match LSE27aA01
21 insignicant match LSE28C01
22 insignicant match LSE28C06
23 GM2 ganglioside activator protein LSE29C07

Total number of rows: 1601

Table truncated, full table size 64 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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