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Platform GPL11074 Query DataSets for GPL11074
Status Public on Oct 22, 2010
Title IATA Lactobacillus casei ATCC 334 2.7k array_v1
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Lacticaseibacillus paracasei ATCC 334
Manufacturer Seccion de Chips de DNA-SCSIE (Universitat de Valencia)
Manufacture protocol Each selected ORF was amplified with specific primers from genomic DNA of Lactobacillus casei ATCC 334. As a general rule, the primers were selected to amplify the complete coding region excepting ORFs exceeding 2.5 kb for which a 2.5 kb internal fragment was amplified. PCR products were analyzed in agarose gels and their sizes estimated by comparison with standard markers. BioGrid (BioRobotics, UK) was used as the spotting robot. Macroarrays were made by printing the PCR products (without purification) onto a positively charged nylon membrane
(Amersham Hybond N+). Printing was done with a 384-pinhead printer, consisting of regular 3 × 3 spots per pin, yielding a total of 3456 available positions. Gene probes were printed in a single replicate. 2390 positions were used for probes, the remaining positions being empty. Membranes were kept humid by setting them onto three Hybond blotting-paper sheets soaked in denaturing solution (1.5M NaCl, 0.5M NaOH). Solid pins of 0.4-mm diameter were used. These pins spot 20 nl each time. PCR products were spotted five times so that each spot contained 20–30 ng DNA in a diameter of approximately 0.6 mm. After printing, the membrane was neutralized with 1.5 M NaCl, 0.5 M Tris/HCl (pH 7.2), 1 mM EDTA (pH 8.0) for 1 min and membranes were kept on filter paper until complete dryness.
Description Nylon membrane (11 x 9 cm) with spotted PCR products up to 2.5 Kb, representing the full-length genes or a 2.5 kb internal fragment for those genes exceeding 2.5 kb for 2390 L.casei genes.
Contributor(s) Zúñiga M
Submission date Oct 20, 2010
Last update date Feb 02, 2011
Contact name Manuel Zúñiga
Phone 34 963900022
Fax 34 963636301
Organization name Instituto de Agroquímica y Tecnología de Alimentos
Department Biotecnología
Lab Bacterias lácticas y Probióticos
Street address Avda. Profesor Agustín Escardino 7
City Paterna
State/province Valencia
ZIP/Postal code 46980
Country Spain
Samples (12) GSM610868, GSM618313, GSM618314, GSM624410, GSM624411, GSM624413 
Series (2)
GSE25448 Comparison of the response to bile of Lactobacillus casei BL23 and its derivative strain TC01
GSE33047 Response to bile of Lactobacillus casei BL23

Data table header descriptions
ORF Locus_tag annotated in the Lactobacillus casei ATCC 334 genome sequence. AND Lactobacillus casei ATCC 334[organism]"
Observations Pseudogenes in L. casei ATCC 334 included in the macroarray are indicated.
SPOT_ID "Empty" indicates non-used positions in the macroarray.

Data table
ID ORF Observations SPOT_ID
R1 - C1 : 1 LSEI_0001
R1 - C3 : 1 LSEI_0002
R1 - C5 : 1 LSEI_0003
R1 - C7 : 1 LSEI_0004
R1 - C9 : 1 LSEI_0005
R1 - C11 : 1 LSEI_0006
R1 - C13 : 1 LSEI_0007
R1 - C15 : 1 LSEI_0008
R1 - C17 : 1 LSEI_0009
R1 - C19 : 1 LSEI_0010
R1 - C21 : 1 LSEI_0011
R1 - C23 : 1 LSEI_0012
R1 - C2 : 1 LSEI_0013
R1 - C4 : 1 LSEI_0014
R1 - C6 : 1 LSEI_0015
R1 - C8 : 1 LSEI_0016
R1 - C10 : 1 LSEI_0017
R1 - C12 : 1 LSEI_0019
R1 - C14 : 1 LSEI_0020
R1 - C16 : 1 LSEI_0021

Total number of rows: 2688

Table truncated, full table size 65 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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