|
| Status |
Public on Nov 21, 2017 |
| Title |
ammonium-deprived, replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
ammonium-deprived, replicate 3
|
| Organism |
Desulfitobacterium hafniense Y51 |
| Characteristics |
cultivation: chemostat
electron acceptor (concentration): Fumarate (65mM)
electron donor (concentration): Lactate (40mM)
medium flow: 19.25 ml/hr
volume: 1050 ml
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Modified version of Macaloid based RNA isolation protocol (Zoetendal et al., 2006: http://0-onlinelibrary-wiley-com.brum.beds.ac.uk/doi/10.1111/j.1365-2958.2006.05056.x/full).
|
| Label |
Cy3
|
| Label protocol |
Five micrograms of total RNA was first reverse-transcribed to cDNA, labelled, and purified using a FairPlay Microarray Labeling Kit according to the one-colour microarray-based prokaryote analysis FairPlay III labelling protocol (Agilent Technologies, ver.1.3).
|
| |
|
| Hybridization protocol |
For each labelled sample, 600 ng of purified dye-coupled cDNA was hybridized to the oligo-microarray at 65 ºC for 16 h following the one-colour microarray-based prokaryote analysis FairPlay III labelling protocol (Agilent Technologies, ver.1.3).
|
| Scan protocol |
Slides were scanned on an Agilent DNA Microarray Scanner G2505C
|
| Description |
US22502548_SLOT02_S01_GE2_107_Sep09_1_1
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition
|
| Data processing |
Outlier spots and spot intensity were extracted with Agilent Feature Extraction software version 10.7.3.1. After background subtraction, mexp and quantile normalization method for within-and inter-array normalization, respectively, were applied using the R-Bioconductor package. Moreover, the normalized values were used of averaging probes replicates and genes replicates.
All the values are presented as transcript intensity transformations of log2 ratio at a given limiting condition to batch condition.
|
| |
|
| Submission date |
Nov 20, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Ye Tian |
| E-mail(s) |
ye.tian@wur.nl
|
| Phone |
+31317480046
|
| Organization name |
Wageningen University
|
| Department |
AFSG
|
| Lab |
The Laboratory of Microbiology
|
| Street address |
Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
6708 WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24288 |
| Series (1) |
| GSE107146 |
Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats |
|
