|
| Status |
Public on Jun 09, 2008 |
| Title |
BAF250b-/- #4B(72hrs) Repl#2 (251411710241) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
BAF250b-/- #4 (72 hrs)
|
| Organism |
Mus musculus |
| Characteristics |
ES
Strain: hybrid of B6,129 and CD1
Gender: unknown sex
Age: 2 months
Development stage: 3.5 dpc blastocysts
Individual Identifier: 251411710241
|
| Extracted molecule |
total RNA |
| Extraction protocol |
One ml of Trizol (Invitrogen) was added to one well. Total RNA was extracted according to the manufacturer's protocol.
|
| 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 |
BAF250b-/- #4 (72 hrs)
|
| 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.
We used 12 new arrays in this Series plus 14 old arrays we submitted earlier (ie, GSM175328-GSM175341). We used only the raw values of Cy3/Cy5 channels in the old arrays to normalize with the 12 new arrays. See VALUE definition below for further details.
|
| |
|
| Submission date |
Sep 10, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Minoru S.H. Ko |
| E-mail(s) |
[email protected]
|
| Phone |
410-558-8359
|
| Organization name |
NIH
|
| Department |
National Institute on Aging
|
| Lab |
Lab of Genetics
|
| Street address |
251 Bayview Blvd, Suite 100, 10C
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL4358 |
| Series (1) |
| GSE8996 |
BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse ES cells |
|
