|
| Status |
Public on Nov 11, 2014 |
| Title |
ribose and glucose, replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
middle of exponential phase cells in SDM + ribose
|
| Organism |
Leuconostoc gasicomitatum LMG 18811 |
| Characteristics |
carbon source: SDM + ribose
|
| Growth protocol |
SDM (20 ml) broth 25°C 20 rpm until cells were middle of exponential phase. SDM media (g/l):tween80 1g, Ammonium citrate 2g, Sodium acetate 5g, MgSO4 * 7H2O 0,1g, MnSO4 0,05g, K2HPO4 2g, Yeast extract 1,5g, Casamino acids 10g. Carbon source inosine, glucose or ribose 20 mM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extacted using acid hot phenol-lithium chloride.
|
| Label |
cy3
|
| Label protocol |
total RNA was used for poly(A) tailing reaction (Ambion/Applied Biosystems). Poly A labeled RNA was in vitro transcribed and labeled with cyanine 3 (Cy3, Invitrogen, Carlsbad, California) and cyanine 5 (Cy5, Invitrogen) using the Amino Allyl MessageAmp™ II aRNA Amplification Kit
|
| |
|
| Channel 2 |
| Source name |
middle of exponential phase cells in SDM + glucose
|
| Organism |
Leuconostoc gasicomitatum LMG 18811 |
| Characteristics |
carbon source: SDM + glucose
|
| Growth protocol |
SDM (20 ml) broth 25°C 20 rpm until cells were middle of exponential phase. SDM media (g/l):tween80 1g, Ammonium citrate 2g, Sodium acetate 5g, MgSO4 * 7H2O 0,1g, MnSO4 0,05g, K2HPO4 2g, Yeast extract 1,5g, Casamino acids 10g. Carbon source inosine, glucose or ribose 20 mM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extacted using acid hot phenol-lithium chloride.
|
| Label |
cy5
|
| Label protocol |
total RNA was used for poly(A) tailing reaction (Ambion/Applied Biosystems). Poly A labeled RNA was in vitro transcribed and labeled with cyanine 3 (Cy3, Invitrogen, Carlsbad, California) and cyanine 5 (Cy5, Invitrogen) using the Amino Allyl MessageAmp™ II aRNA Amplification Kit
|
| |
|
| |
| Hybridization protocol |
Labeled amino allyl RNA (aaRNA) was fragmented at 60°C for 30 min using Gene Expression Hybridization kit (Agilent). Hybridization was performed at 65 °C with 20 rpm rotation for 16 h.
|
| Scan protocol |
Scanned on an Axon 4200 AL scanner
|
| Description |
Biological replicate 2 of 3 L. gasicomitatum type strain growth on ribose or glucose
|
| Data processing |
R with limma package
|
| |
|
| Submission date |
Jan 22, 2014 |
| Last update date |
Nov 12, 2014 |
| Contact name |
Elina Jääskeläinen |
| E-mail(s) |
[email protected]
|
| Phone |
+358 2941 57167
|
| Organization name |
University of helsinki
|
| Department |
Food Hygiene and Environmental Health
|
| Street address |
P.O. Box 66 (Agnes Sjöbergin katu 2)
|
| City |
Helsinki |
| ZIP/Postal code |
00014 University of Helsinki |
| Country |
Finland |
| |
|
| Platform ID |
GPL16127 |
| Series (1) |
| GSE54273 |
Gene expression of Leuconostoc gasicomitatum LMG18811T during growth on glucose, ribose or inosine |
|
