|
| Status |
Public on Jul 16, 2008 |
| Title |
Crypt LCM LOI(+) rep3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Crypt_LCM_LOI(+)
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57BL/6
Gender: male
Age: 120 days
Development stage: adult
Individual Identifier: LOI(+)3 251279910119
|
| Biomaterial provider |
Dr. Andrew Feinberg
|
| Treatment protocol |
The mouse was euthanized by CO2 inhalation and the small intestine was collected and washed with PBS. Pieces of the middle part of the small intestine were collected and frozen at -80C, embedded in OCT, sectioned at 10um, and fixed with 70% EtOH on the slides. Slides were stained with hematoxylin, dehydraded and used for LCM within one week. 5,000 to 13,000 intestinal crypts were dissected by LCM, and RNA was extracted using RNeasy (QIAGEN).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted from microdissected crypts using RNeasy as directed by manufacturer. Samples QCs on an Agilent Bioanalyzer for RNA quality and quantity.
|
| 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).
|
| |
|
| 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 |
Crypt_LCM_LOI(+)
|
| 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 |
Jul 25, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Andrew Feinberg |
| E-mail(s) |
afeinberg@jhu.edu
|
| Phone |
4106143489
|
| Fax |
4106149819
|
| Organization name |
Johns Hopkins University
|
| Department |
Medicine
|
| Lab |
Center for Epigenetics
|
| Street address |
720 Rutland Ave., 1064 Ross
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL2552 |
| Series (1) |
| GSE8583 |
Gene expression changes in the intestinal crypts of mice with loss of imprinting |
|
