|
| Status |
Public on Jun 01, 2015 |
| Title |
SC4B_LP-SC3X_LP |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
SC4B_LP
|
| Organism |
Daphnia pulex |
| Characteristics |
clone id: SC4B
genotype: contemporary (~10-yr-old clone)
dietary group: LP (low P; C:P~120)
tissue: whole body
|
| Growth protocol |
20 C, 16:8 light: dark cycle, 1 mg C/L Scenedesmus algae at high or low phoshourus levels
|
| Extracted molecule |
total RNA |
| Extraction protocol |
First, tissue is homogenized with Trizol Reagent (Ambion). Then RNA is extract with phenol and precipitated with Ethanol. The precipitate is captured and washed using Qiagen Rneasy spin column.
|
| Label |
Cy3
|
| Label protocol |
target protocol: Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations. aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with Invitrogen's ChargeSwitch Kit.
quality assessement protocol: Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.
ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com
|
| |
|
| Channel 2 |
| Source name |
SC3X_LP
|
| Organism |
Daphnia pulex |
| Characteristics |
clone id: SC3X
genotype: ancient (~700-yr-old clone)
dietary group: LP (low P; C:P~120)
tissue: whole body
|
| Growth protocol |
20 C, 16:8 light: dark cycle, 1 mg C/L Scenedesmus algae at high or low phoshourus levels
|
| Extracted molecule |
total RNA |
| Extraction protocol |
First, tissue is homogenized with Trizol Reagent (Ambion). Then RNA is extract with phenol and precipitated with Ethanol. The precipitate is captured and washed using Qiagen Rneasy spin column.
|
| Label |
Cy5
|
| Label protocol |
target protocol: Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations. aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with Invitrogen's ChargeSwitch Kit.
quality assessement protocol: Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.
ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com
|
| |
|
| |
| Hybridization protocol |
Hybridization and post-hybridization washing using Hybridization Systems Kit (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com
|
| Scan protocol |
Image acquisition with Roche NimbleGen MS200 Scanner, 2 micron resolution.
|
| Data processing |
Raw signal intensities extracted with NimbleScan 2.6 Software (Roche NimbleGen) as PAIR files.
|
| |
|
| Submission date |
Jun 24, 2013 |
| Last update date |
Jun 01, 2015 |
| Contact name |
Jacqueline Lopez |
| E-mail(s) |
jacqueline.ann.lopez@gmail.com
|
| Phone |
574-631-1902
|
| Organization name |
University of Notre Dame
|
| Department |
Biology
|
| Lab |
Pfrender Laboratory
|
| Street address |
019 Galvin Life Science Center
|
| City |
Notre Dame |
| State/province |
Indiana |
| ZIP/Postal code |
46556 |
| Country |
USA |
| |
|
| Platform ID |
GPL11278 |
| Series (1) |
| GSE48232 |
Identifying genes and pathways that respond differently to dietary C:P between old (~700-yr-old) and young (~10-yr-old) resurrected Daphnia pulicaria genotypes that differ in C and P physiology |
|
