|
| Status |
Public on Dec 07, 2010 |
| Title |
Lymph node-naive-TB-tnf 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
TB
|
| Organism |
Mus musculus |
| Characteristics |
Strain: TB-TNF KO double
Gender: female
Development stage: adult
Genetic modification: gene knock out
Individual Identifier: 251279910181
|
| Biomaterial provider |
Sergei Grivennikov grivennikovs@ncifcrf.gov 301-846-6449
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pooled Lymph nodes were immediately frozen in luquid N2 and RNA was prepared using Tri-reagent according to manufacturer recommendations. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in DEPC dH2O. After that RNA was precipitated by LiCL and dissolved in DEPC water. 2 microgram of total RNA were taken for microarray analysis.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.
|
| |
|
| Channel 2 |
| Source name |
Universal Mouse Reference Cell Line Pool
|
| Organism |
Mus musculus |
| Characteristics |
Universale Mouse Reference
|
| Biomaterial provider |
Stratagene
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts
|
| Label |
Cy5
|
| Label protocol |
Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).
|
| |
|
| |
| Hybridization protocol |
Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004. Agilent Publication Number: G4140-90030 V4.1 APRIL 2004.
|
| Scan protocol |
Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um. A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format. Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696
|
| Description |
TB
|
| Data processing |
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
|
| |
|
| Submission date |
Jul 27, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Sergei I Grivennikov |
| Organization name |
National Cancer Institute
|
| Lab |
Basic Research Laboratory
|
| Street address |
P.O. Box B
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL2552 |
| Series (1) |
| GSE8610 |
Genes regulated by T cell and B cell derived TNF in naive lymph nodes |
|
