|
| Status |
Public on Aug 07, 2014 |
| Title |
BF638R DM-mucin media rep1 |
| Sample type |
RNA |
| |
|
| Source name |
grown in vitro to mid-log phase in defined media with mucin glycans
|
| Organism |
Bacteroides fragilis 638R |
| Characteristics |
treatment: grown in vitro to mid-log phase in defined media with mucin glycans
sample type: grown in vitro to mid-log phase in defined media with mucin glycans
|
| Growth protocol |
For in vitro samples: Overnight cultures of Bacteroides fragilis 638R were diluted into defined media contain either 0.5% glucose or 2% mucin glycans, and grown to mid-logarithmic phase at A550 of 0.5 complex media ( Rocha et al. 1996, J. Bacteriol. 178:6895). For in vivo samples, BF638R cells were grown in a tissue cage in rats and sampled on days 1,4, and 8 post-inoculation as described by Lobo et al. 2013, MicrobiologyOpen 2:326.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the hot phenol method and treated as described by Sund et al, 2008, Mol. Microbiol.67:129-142.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142).
|
| |
|
| Hybridization protocol |
Hybridization was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)
|
| Scan protocol |
Scanning was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)
|
| Data processing |
Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) using NimbleGen Systems DEVA 1.1 software as described on their web site. Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) using DEVA 1.1 software downloaded from Roche/NimbleGen as described on their web site (http://www.nimblegen.com/downloads/support/06271090001_DEVA_UserGuide_v1p2.pdf).
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| |
|
| Submission date |
Jan 07, 2014 |
| Last update date |
Aug 07, 2014 |
| Contact name |
Charles Jeffrey Smith |
| E-mail(s) |
[email protected]
|
| Phone |
252-744-2700
|
| Fax |
252-744-3104
|
| Organization name |
East Carolina University
|
| Department |
Microbiology & Immunology
|
| Street address |
600 Moye Blvd.
|
| City |
Greenville |
| State/province |
NC |
| ZIP/Postal code |
27834 |
| Country |
USA |
| |
|
| Platform ID |
GPL15788 |
| Series (2) |
| GSE53883 |
Bacteroides fragilis in vivo gene expression |
| GSE73107 |
Cis-encoded sRNAs repress expression of polysaccharide utilization loci in Bacteroides fragilis 638R |
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