|
| Status |
Public on Aug 06, 2010 |
| Title |
BWH_Comstock_B_fragilis_9343_glycoprotein_study_delta-gmd-fcl_delta-fkp_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp
|
| Organism |
Bacteroides fragilis NCTC 9343 |
| Characteristics |
Accession: NC_003228 + NC_006873
GI: 60679597 + 60650141
Taxname: Bacteroides fragilis NCTC 9343
Taxid: 272559
Genome_ID: 644 + 18259
This sample is from a double deletion mutant in which the adjacent genes gmd (BF1888) and fcl (BF1887) are deleted, and a second deletion removed fkp (BF2607).
|
| Biomaterial provider |
Comstock Laboratory, Maria Chatzidaki-Livanis
|
| Treatment protocol |
The delta-gmd-fcl mutant was constructed by deleting 2,092 bp of DNA, affecting both of the adjacent genes (BF1887 [fcl] and BF1888 [gmd]). The DNA removed by the gmd-fcl deletion corresponds to bases 2,205,448 through 2,207,539 of NC_003228. A second deletion encompassing 2,791 bp of the 2,850 bp fkp gene (BF2607) was introduced into the delta-gmd-fcl background, resulting in the B. fragilis delta-gmd-fcl delta-fkp strain. The bases deleted by the delta-fkp mutation correspond to 3,033,425 through 3,036,215 of NC_003228.
|
| Growth protocol |
Bacteroides fragilis NCTC 9343 was grown to mid-log phase (O.D.600nm ~0.75) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in basal media (Pantosti et al. Infect. Immun. 59(6):2075).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by Roche NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
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| |
|
| Hybridization protocol |
Hybridization was performed by Roche NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by Roche NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp. It is the second of three biological replicates of this mutant strain used in this experiment, each from separate cultures.
|
| Data processing |
The normalized values were calulated by NimbleGen Systems Inc. using quantile normalization (Bolstad et al. Bioinformatics 19(2):185) and the RMA algorithm (Irizarry et al. Biostatistics 4(2):249) with tools made available by the Bioconductor project (http://www.bioconductor.org).
Further explanation of Nimblegen data types is available in the NimbleScan User's Guide at: http://www.nimblegen.com/products/lit/nimblescan2.3usersguide.pdf
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| |
|
| Submission date |
Aug 13, 2008 |
| Last update date |
Aug 07, 2009 |
| Contact name |
Michael J Coyne |
| E-mail(s) |
mcoyne@channing.harvard.edu
|
| Phone |
617-525-7820
|
| Organization name |
Brigham & Women's Hospital
|
| Department |
Medicine
|
| Lab |
Channing Laboratory
|
| Street address |
181 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL7163 |
| Series (1) |
| GSE12440 |
Expression analysis of Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp and B. fragilis NCTC 9343 delta-lfg |
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