|
| Status |
Public on Dec 01, 2012 |
| Title |
IST408, genomic |
| Sample type |
genomic |
| |
|
| Source name |
IST408 wild-type grown in S medium overnight
|
| Organism |
Burkholderia cepacia |
| Characteristics |
isolate: IST408
genotype: wild-type
|
| Treatment protocol |
Bacterial cells were resuspended in RNAprotect Bacteria Reagent (Qiagen).
|
| Growth protocol |
Bacteria were grown in S medium overnight.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted from bacterial cells using the DNeasy blood and tissue kit (Qiagen) following the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
For DNA analysis, a total of 1.5 ug of genomic DNA from B. cepacia IST408 was labeled using the Bioprime DNA labelling System (Invitrogen,Paisley, UK) following a strategy for genomic DNA hybridization to GeneChips developed by Hammond and co-authors (2005). Cleanup was performed using the MinElute PCR Purification Kit (Qiagen, Hilden), and quality was checked on an Agilent 2100 Bioanalyzer using a DNA 1000 assay.
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 µg of end-labeled fragmented DNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 50ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.
|
| Description |
Mucoid wild-type clinical strain.
The CEL file for this Sample was analyzed in Xspecies DNA hyb CDF batchmaker v3.2 to generate Bcc1sa520656F_Xspecies.CEL80.cdf. This Sample does not have processed data.
|
| Data processing |
DNA-based probe-selection was performed using Xspecies DNA hyb CDF batchmaker v3.2, available here: http://affymetrix.arabidopsis.info/xspecies/. An optimal signal cutoff of 80 and minimum number of probes per probe set of 7 were determined empirically, resulting in the masking of 24223 of the original 226576 probes on the array and the exclusion of 156 probe sets. The new cdf file created (Bcc1sa520656F_Xspecies.CEL80.cdf) was used in DNA-Chip Analyzer 2008 for the subsequent gene expression analyses.
|
| |
|
| Submission date |
May 23, 2012 |
| Last update date |
Dec 01, 2012 |
| Contact name |
Leonilde Morais Moreira |
| E-mail(s) |
lmoreira@ist.utl.pt
|
| Phone |
+351 218419031
|
| Organization name |
Instituto Superior Tecnico
|
| Department |
Bioengineering
|
| Lab |
Biological Sciences
|
| Street address |
A. Rovisco Pais
|
| City |
Lisboa |
| ZIP/Postal code |
1049-001 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL15600 |
| Series (1) |
| GSE38183 |
Expression data from Burkholderia cepacia IST408 bceE and bceF mutants |
|
