|
| Status |
Public on Aug 01, 2017 |
| Title |
WT vs ΔlancRNA ΔHTH Expo1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wild-type pure culture
|
| Organism |
Ligilactobacillus salivarius UCC118 |
| Characteristics |
genotype: wild-type
growth: Stationnary
|
| Growth protocol |
MRS broth, 37°C, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA, Rneasy kit (Qiagen) following manufacturer's instructions + DNA digestion (Turbo Dnase, Ambion) following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Reverse Transcription on 7 µg RNA and labelling on 500 ng cDNA
|
| |
|
| Channel 2 |
| Source name |
ΔlancRNA ΔHTH mutant pure culture
|
| Organism |
Ligilactobacillus salivarius UCC118 |
| Characteristics |
genotype: ΔlancRNA ΔHTH
growth: Stationnary
|
| Growth protocol |
MRS broth, 37°C, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA, Rneasy kit (Qiagen) following manufacturer's instructions + DNA digestion (Turbo Dnase, Ambion) following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Reverse Transcription on 7 µg RNA and labelling on 500 ng cDNA
|
| |
|
| |
| Hybridization protocol |
Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050)
|
| Scan protocol |
Slides were scanned using an Agilent Microarray Scanner System (G2505B) with Agilent scan control software version 7.0 for the 44k microarray at a resolution of 5 microns. Agilent feature extraction software version 9.1 was used to process the image file from the scanner
|
| Description |
WT vs ΔlancRNA ΔHTH in exponential growth phase Replicate 1
Biological replicate 1 of 2
|
| Data processing |
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction.
|
| |
|
| Submission date |
Dec 22, 2016 |
| Last update date |
Aug 01, 2017 |
| Contact name |
Denise B Lynch |
| E-mail(s) |
lynchde@gmail.com
|
| Phone |
0851309959
|
| Organization name |
University College Dublin
|
| Department |
APC Microbiome Institute
|
| Lab |
Paul O'Toole
|
| Street address |
College Road
|
| City |
Cork |
| State/province |
Not Applicable |
| ZIP/Postal code |
T12 YT20 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL22845 |
| Series (1) |
| GSE92837 |
A long and abundant non-coding RNA (lancRNA) in Lactobacillus salivarius |
|
