|
| Status |
Public on Jun 22, 2009 |
| Title |
E601 mucin 3 |
| Sample type |
RNA |
| |
|
| Source name |
Pseudomonas aeruginosa E601 grown with human colon cell line mucin LS174T as S source
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
Pseudomonas aeruginosa strain E601, a cystic fibrosis isolate with mucin sulfatase activity
|
| Biomaterial provider |
Kertesz laboratory, University of Manchester
|
| Treatment protocol |
no treatment
|
| Growth protocol |
5 ml cultures of cells were grown aerobically in succinate-based minimal medium in 50 ml flasks shaken with 220 rpm at 37 C. Cells were grown with 500 uM Sulfate in repeated batch cultures for at least 20 generations. The cells were then grown for at least 12 generations with 25 ug/ml human colon cell line mucin LS174T as sulfur source.These cells were then used to inoculate the starter culture needed for RNA preparation, grown with 25 ug/ml LS174T mucin as S source). For the preparation of RNA a 5 ml culture was started with 100 ul of a freshly grown culture. and grown to an OD600 of 0.2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy mini kit – bacterial protocol. The washing step with 700 ul of buffer RW1 was split up into 2 steps and an on column digest of DNA using Qiagen DNase was performed in between
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix procedures, starting with 5-10 ug RNA
|
| |
|
| Hybridization protocol |
Standard Affymetrix procedures
|
| Scan protocol |
Standard Affymetrix procedures
|
| Description |
no treatment
|
| Data processing |
Analysis based on GC-RMA normalization of the data in the CEL files
|
| |
|
| Submission date |
Jul 09, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Michael A. Kertesz |
| E-mail(s) |
michael.kertesz@manchester.ac.uk
|
| Organization name |
University of Manchester
|
| Department |
Faculty of Life Sciences
|
| Street address |
Oxford Rd
|
| City |
Manchester |
| ZIP/Postal code |
M13 9PT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE8408 |
Transcriptomic analysis of the sulfate starvation response in Pseudomonas aeruginosa |
|
