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Status |
Public on Nov 21, 2017 |
Title |
ammonium-deprived, replicate 1 |
Sample type |
RNA |
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Source name |
ammonium-deprived, replicate 1
|
Organism |
Desulfitobacterium hafniense Y51 |
Characteristics |
cultivation: chemostat electron acceptor (concentration): Fumarate (60mM) electron donor (concentration): Lactate (40mM) medium flow: 18.8 ml/hr volume: 1020 ml
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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).
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Hybridization protocol |
For each labelled sample, 600 ng of purified dye-coupled cDNA was hybridized to the oligo-microarray at 65 ÂșC for 16 h following the one-colour microarray-based prokaryote analysis FairPlay III labelling protocol (Agilent Technologies, ver.1.3).
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Scan protocol |
Slides were scanned on an Agilent DNA Microarray Scanner G2505C
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Description |
US22502548_SLOT01_S01_GE2_107_Sep09_2_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
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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.
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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 |
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Platform ID |
GPL24288 |
Series (1) |
GSE107146 |
Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats |
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