|
| Status |
Public on Jul 30, 2014 |
| Title |
Control vs. Tellurite replicate2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA extracted from tellurite exposed cultures
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
strain: BW 25113
|
| Treatment protocol |
Cultures were exposed to tellurite (0.5 µg/ml) during 15 min and incubated to 37 °C with vigorous shaking
|
| Growth protocol |
An overnight E. coli culture was inoculated (in a 1:1000 dilution) in fresh LB containing flasks and incubated with vigorous shaking to 37 °C. At an OD600 ~0.4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Rneasy Mini Kit (Qiagen) following manufacturer's instructions
|
| Label |
Alexa Fluor 647
|
| Label protocol |
20 µg of total RNA were primed with 2 µl of 3 µg/µl Random primer at 80°C for 5 min, then reversed transcribed at 42°C for 2.5 h in the presence of 200 U SuperScript II Reverse transcriptase (Invitrogen), and 10 mM each dATP, dCTP, dGTP, with 4 mM dTTP, 1 mM Alexa fluor 555 aha dUTP (or 1mM Alexa fluor 647 aha dUTP)
|
| |
|
| Channel 2 |
| Source name |
Total RNA extracted from untreated cultures
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
strain: BW 25113
|
| Treatment protocol |
Cultures were exposed to tellurite (0.5 µg/ml) during 15 min and incubated to 37 °C with vigorous shaking
|
| Growth protocol |
An overnight E. coli culture was inoculated (in a 1:1000 dilution) in fresh LB containing flasks and incubated with vigorous shaking to 37 °C. At an OD600 ~0.4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Rneasy Mini Kit (Qiagen) following manufacturer's instructions
|
| Label |
Alexa Fluor 555
|
| Label protocol |
20 µg of total RNA were primed with 2 µl of 3 µg/µl Random primer at 80°C for 5 min, then reversed transcribed at 42°C for 2.5 h in the presence of 200 U SuperScript II Reverse transcriptase (Invitrogen), and 10 mM each dATP, dCTP, dGTP, with 4 mM dTTP, 1 mM Alexa fluor 555 aha dUTP (or 1mM Alexa fluor 647 aha dUTP)
|
| |
|
| |
| Hybridization protocol |
Hybridization buffer (6X SSC buffer; 0.2 % SDS; 5 % Denhardt's solution; Salmon sperm DNA 13 µg/ml; 25 % deionized formamide; 23 µl of tagged cDNA) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially
|
| Scan protocol |
Slides were scanned on a ScanArray Gx scanner (PerkinElmer).
|
| Description |
Biological replicate 2 of 2 (Dye swap)
|
| Data processing |
LOESS normalized, Normexp background subtracted data obtained from log2 of processed target/reference signal. Limma package used implemented in Bioconductor
|
| |
|
| Submission date |
Jun 03, 2014 |
| Last update date |
Jul 30, 2014 |
| Contact name |
David Enrique Loyola |
| E-mail(s) |
dloyolac@gmail.com
|
| Phone |
+56-9-74305392
|
| Organization name |
OMICS Solutions, Centro Nacional de Genómica y Bioinformática
|
| Street address |
Avenida Libertador Bernardo O'Higgins 340
|
| City |
Santiago |
| State/province |
Santiago |
| ZIP/Postal code |
8331150 |
| Country |
Chile |
| |
|
| Platform ID |
GPL15818 |
| Series (1) |
| GSE58176 |
Transcriptional profiling of E. coli cultures exposed to tellurite 0.5 µg/ml |
|
