|
| Status |
Public on Aug 30, 2005 |
| Title |
TS cells, sample #3(16011321011192) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
TS cells
|
| Organism |
Mus musculus |
| Characteristics |
TS cells 129/Sv male gene knock in
|
| Biomaterial provider |
Dr. Tilo Kunath
|
| Growth protocol |
The cells derived form ICR E3.5 blastocysts and the extraembryonic ectoderm of E6.5 embryos, cultured in the presence of feeder-conditioned medium with FGF4; see Tanaka et al. Science 1998.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Using the QIAGEN RNeasy midi kit (QIAGEN Inc., Santa Clarita, CA), total RNA was extracted from the diploid-sorted TS cell lines derived from ICR E3.5 blastcysts and the extraembryonic ectoderm of E6. 5 embryos, cultured in the presence of feeder-conditioned medium with FGF4 (details on Tanaka et al. 1998. Science 282: 2072-2075).
|
| Label |
Cy3
|
| 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).
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| |
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| Channel 2 |
| Source name |
Universal Mouse Reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
Universale Mouse Reference
|
| Biomaterial provider |
Mark Carter
|
| 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).
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| |
|
| |
| 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. The manual can be found at https://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=34961, or through a WEB search on the manual title.
|
| 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
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| Description |
TS cells
|
| 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.
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| |
|
| Submission date |
Aug 27, 2005 |
| Last update date |
Feb 05, 2007 |
| 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 |
GPL870 |
| Series (1) |
| GSE3214 |
High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridiz |
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