|
| Status |
Public on Nov 30, 2011 |
| Title |
Pf0-1_whole_genome_array_wildtype_adnA_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Pseudomonas fluorescens Pf0-1 wild-type
|
| Organism |
Pseudomonas fluorescens Pf0-1 |
| Characteristics |
genotype: Wild-type
phenotype: normal
|
| Growth protocol |
Pseudomonas fluorescens Pf0-1 (adnA+) was grown overnight in 50 mL of Pseudomonas Minimal Medium (PMM) Kirner, S., S et. al. 1996. Microbiology 142 ( Pt 8):2129-2135.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were treated with the RNAprotect reagent (Qiagen Inc., Valencia, CA, USA) and the total RNA was extracted using the RNeasy Mini kit (Qiagen). RNA was treated with RQ1 RNase free DNase (Promega Corporation, Madison, WI, USA). RNA samples were quantified using a NanoDrop Spectrophotometer (Isogen Life Science, The Netherlands). The quality of the RNA was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) at Tufts University Core Facility (Tufts University School of Medicine, Boston, MA, USA). First strand cDNA was synthesized from 10 mg total RNA with random hexamer primers from Invitrogen (Carlsbad, CA) using SuperScript Double-Stranded cDNA Synthesis kits (Invitrogen Corporation, Carlsbad, California, USA). The cDNA synthesis was carried out according to the NimbleGen protocol for synthesis of doublestranded cDNA.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of wild-type Pseudomonas fluorescens Pf0-1. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Nov 22, 2011 |
| Last update date |
Nov 30, 2011 |
| Contact name |
Matthew Mastropaolo |
| E-mail(s) |
Matthew.Mastropaolo@tufts.edu
|
| Organization name |
Tufts Universicty School of Medicine
|
| Department |
Molecular Biology and Microbiology
|
| Lab |
Center for Adaptation Genetics and Drug Resistance, Levy Lab
|
| Street address |
136 Harrison Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02111 |
| Country |
USA |
| |
|
| Platform ID |
GPL14909 |
| Series (1) |
| GSE33865 |
Expression analysis of the AdnA regulon in Pseudomonas fluorescens Pf0-1 |
|
