|
| Status |
Public on Mar 04, 2020 |
| Title |
B.subtilis_t = 330_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Bacillus subtilis wild type
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: PY79
development phase: vegetative cell
|
| Growth protocol |
Purified spores were heat activated (HA) (70°C for 30 min) prior to germination. The spores were suspended at 4.5* 10˄10 spores/ml in MOPS liquid minimal medium (pH 7.4) supplemented with a mixture of AGFK (10mM L-asparagine, 10mM D-glucose, 1mM D-fructose, 1mM KCl) and 10mM L-alanine. Throughout the spore revival, samples were drawn at regular time intervals for further analysis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy MinElute Cleanup kit from Qiagen and DNA was removed by Turbo DNA-free kit (Ambion Inc., Applied Biosystems, USA). The purity and quantity of isolated RNA were checked spectrophotometrically on a NanoDrop spectrophotometer (ND-1000, Isogen Life Science, NL).
|
| 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 |
Each hybridization mixture comprised 1.1 μg Test (Cy3) and 1.1 μg Reference (Cy5), a common reference pool of all samples. Microarrays were with the NimbleGen Hybridization System (Roche NimbleGen).
|
| Scan protocol |
Scanning was performed by NimbleScan v2.6 (Roche NimbleGen).
|
| Data processing |
For the raw data Log2 ratios were calculated for each feature and gene expression values were calculated using the median polish algorithm
|
| |
|
| Submission date |
Mar 03, 2020 |
| Last update date |
Mar 04, 2020 |
| Contact name |
Bhagyashree Swarge |
| E-mail(s) |
b.n.swarge@uva.nl
|
| Organization name |
Swammerdam institute of life sciences, University of Amsterdam
|
| Street address |
Science park 908
|
| City |
Amsterdam |
| State/province |
North Holland |
| ZIP/Postal code |
1098XH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16974 |
| Series (1) |
| GSE146277 |
Intergrative analysis of proteome and transcriptome dynamics during Bacillus subtilis spore revival |
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