|
| Status |
Public on Apr 23, 2009 |
| Title |
Gene expression in GLN vs PDLN (NOD mouse #2) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
NOD GLN
|
| Organism |
Mus musculus |
| Characteristics |
tissue: gastric lymph node (left pancreatic lymph node)
strain: NOD
sex: female
age: 12 wk old
|
| Biomaterial provider |
Jackson Laboratories
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gastric lymph node was excised and immediately homogenized in Trizol Reagent. RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA purity and quality was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific), Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
RNA was amplified, labeled with Cy5 and combined with spike B using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies). The amplified cRNA was purified using the RNeasy kit (Qiagen), and specific activity was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific).
|
| |
|
| Channel 2 |
| Source name |
NOD PDLN
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pancreatico-duodenal lymph node (right pancreatic lymph node)
strain: NOD
sex: female
age: 12 wk old
|
| Biomaterial provider |
Jackson Laboratories
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pancreatico-duodenal lymph node was excised and immediately homogenized in Trizol Reagent. RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA purity and quality was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific), Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
RNA was amplified, labeled with Cy3 and combined with spike A using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies). The amplified cRNA was purified using the RNeasy kit (Qiagen), and specific activity was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific).
|
| |
|
| |
| Hybridization protocol |
Two color microarrays were performed using the whole mouse genome 4x44K Oligo microarray kit (Agilent, series 2514868). Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65C, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.
|
| Scan protocol |
Microarray chips were scanned using the DNA microarray scanner (Agilent) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software.
|
| Description |
No additional information.
|
| Data processing |
Data was processed using GeneSpring GX 10 Software. Data was imported using the enhanced Agilent FE Import setting. Spot information in Feature Extraction was used to flag data, and normalization was performed using "per spot and per chip: intensity dependent (Lowess) normalization". Data obtained for the Cy5-labelled GLN sample were divided by the Cy3-labelled PDLN sample to obtain ratios shown in the "PRE_VALUE" column of processed data. Raw data show log2 of ratio.
|
| |
|
| Submission date |
Apr 21, 2009 |
| Last update date |
Apr 22, 2009 |
| Contact name |
Remi J Creusot |
| E-mail(s) |
rcreusot@stanford.edu
|
| URL |
http://fathmanlab.stanford.edu/people/index.html
|
| Organization name |
Stanford University
|
| Department |
Medicine
|
| Lab |
Fathman
|
| Street address |
269 Campus Dr, CCSR 2240
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (2) |
| GSE15753 |
Gene expression in GLN versus PDLN in NOD mice |
| GSE15784 |
Lymphoid tissue specific homing of bone marrow-derived dendritic cells |
|
