|
| Status |
Public on Feb 20, 2009 |
| Title |
WT Footpad E15.5-1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Footpads
strain: C57BL/6
gender: male
age: E15.5
development stage: E15.5
genetic modification: Wild-type
individual identifier: 251508710417A1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were isolated by Trizol by standard protocol (Invitorogen). RNA samples were then subjected to LiCl precipitation to eliminate genomic DNA contamination.
|
| 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 |
Universal 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 |
Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1, August 2006)
|
| Scan protocol |
Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.
|
| Description |
WT Footpad E15.5-1
|
| 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.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 4 arrays in the series: AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin
|
| |
|
| Submission date |
Feb 17, 2009 |
| Last update date |
Feb 20, 2009 |
| Contact name |
Chang-Yi Cui |
| E-mail(s) |
cuic@mail.nih.gov
|
| Phone |
410-558-8129
|
| Organization name |
NIH
|
| Department |
NIA
|
| Lab |
Lab of Genetics
|
| Street address |
251 Bayview Blvd Suite 100, 10C222
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL6867 |
| Series (2) |
| GSE14870 |
Requirement for Shh and Fox family genes at different stages in sweat gland development (E15.5) |
| GSE14907 |
Requirement for Shh and Fox family genes at different stages in sweat gland development |
|
