|
| Status |
Public on Apr 23, 2009 |
| Title |
Gene expression in PLN vs ILN (FVB) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
FVB PLN
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
sample: Pooled tissue from 5 mice
tissue: pancreatic lymph nodes
|
| Biomaterial provider |
Jackson Laboratories
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
pancreatic lymph nodes were 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 |
FVB ILN
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
sample: Pooled tissue from 5 mice
tissue: inguinal lymph nodes
|
| Biomaterial provider |
Jackson Laboratories
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
inguinal lymph nodes were 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 Oligo microarray kit (Agilent, series 2512694). 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 process using GeneSpring GX 7.3 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 PLN sample were divided by the Cy3-labelled ILN sample to obtain ratios shown in the "PRE_VALUE" column.
|
| |
|
| Submission date |
Apr 20, 2009 |
| Last update date |
Apr 24, 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 |
GPL7042 |
| Series (2) |
| GSE15748 |
Gene expression in PLN vs. ILN or MLN in mice |
| GSE15784 |
Lymphoid tissue specific homing of bone marrow-derived dendritic cells |
|
