|
| Status |
Public on Mar 17, 2009 |
| Title |
21/1 |
| Sample type |
genomic |
| |
|
| Source name |
Lactobacillus casei 21/1, plant
|
| Organism |
Lacticaseibacillus casei |
| Characteristics |
ecological niche of isolation: plant materials (silage)
strain: 21/1
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
Lactobacillus casei strains were prepared from frozen stock by two transfers in MRS broth (BD Biosciences), without shaking, for 16–18 h at 37 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using a MasterPureTM Gram Positive DNA Purification Kit (Epicentre, Madison, WI).
|
| Label |
biotin
|
| Label protocol |
Five micrograms of genomic DNA was fragmented and labeled according to instructions for labeling mRNA for antisense prokaryotic arrays (Affymetrix Inc.).
|
| |
|
| Hybridization protocol |
Reactions containing 1 μg labeled DNA were used for hybridization at the Utah State University Center for Integrated Biosystems Affymetrix core facility (Logan, UT).
|
| Scan protocol |
Genechips were scanned using Affmetrix GeneChip Scanner 3000.
|
| Description |
Comparative genome hybridization
|
| Data processing |
Statistical analysis of microarray data was done by R (www.r-project.org). Array images were reduced to intensity values for each probe and all arrays that met acceptable quality control criteria were used for further analysis. Array pre-processing (background correction, normalization, and summarization) was performed using the Robust Multi-array Average (RMA) method (Bolstad et al. 2003) using Bioconductor (http://www.bioconductor.org). Cutoff values for presence/absence determination were selected empirically based on hybridization signal intensity from negative (Lb. helveticus CNRZ 32) and positive (from hybridization with Lb. casei ATCC 334 DNA) probe controls. The cutoff value set for this dataset is 5.3.
|
| |
|
| Submission date |
Mar 16, 2009 |
| Last update date |
Mar 16, 2009 |
| Contact name |
Hui Cai |
| E-mail(s) |
hcai2@wisc.edu
|
| Organization name |
University of Wisconsin
|
| Street address |
1605 Linden Dr
|
| City |
Madison |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL8309 |
| Series (1) |
| GSE15030 |
Comparative genome hybridization for Lactobacillus casei |
|
