|
| Status |
Public on May 11, 2007 |
| Title |
EG-3 passage 9 Lif-(251279910201) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
EG-3 passage 9 Lif-
|
| Organism |
Mus musculus |
| Characteristics |
embryonic germ cell
Strain: 129Sv
Gender: female
|
| Growth protocol |
EG grown on gelatin coated, 6-well plates, 200000 cells/well (20000 cells/cm2), in complete ES medium: DMEM, 15% FBS;1mM sodium pyruvate; 0.1 mM NEAA, 2 mM glutamate,0.1 mM beta-mercapto ethanol,penicillin/streptomycin. Cells were incubated at 37 0C; 5% CO2. Medium was changed daily. On the day 3 Trizol was added and RNA extracted.nt and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 30 ul of DEPC dH2O.
|
| 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 RNA
|
| Organism |
Mus musculus |
| Characteristics |
Universale Mouse Reference
|
| Growth protocol |
The UMRR is provided in a solution of 70% ethanol and 0.1 M sodium acetate. Prepare the UMRR for use as follows: 1.Centrifuge the tube at 12,000 x g for 15 minutes at 4C. 2.Carefully remove the supernatant. 3.Wash the pellet in 70% ethanol. 4.Centrifuge the tube at 12,000 x g for 15 minutes at 4C. 5.Carefully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.
|
| 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)
|
| Description |
TGC(Embryonic germ cells)
|
| Data processing |
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See NIA Array Analysis website for details.
|
| |
|
| Submission date |
Sep 26, 2006 |
| Last update date |
May 11, 2007 |
| Contact name |
Minoru S.H. Ko |
| E-mail(s) |
kom@mail.nih.gov
|
| 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 |
GPL2552 |
| Series (1) |
| GSE5914 |
Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells |
|
