|
| Status |
Public on Oct 01, 2009 |
| Title |
pylorus at E16.5, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
pylorus tissue from E16.5 mouse embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pylorus
strain: C57Bl/6J
age: E16.5
developmental stage: embryo
|
| Treatment protocol |
For the microarray experiment, a total of 174 E14.5 embryos and 95 E16.5 embryos were dissected, and for each time/tissue group (eg, E14.5 duodenum; six groups total), collected tissue was randomly pooled into one of three samples for replicate analysis.
|
| Growth protocol |
Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine and stomach were removed and three contiguous segments were collected from antrum (stomach), pylorus, and duodenum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions. Separate collections were performed for RT-PCR validation of microarray results.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized to MOE 430.2 microarrays (eighteen total chips: six time/tissue groups, three replicate chips for each group; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from pylorus tissue from E16.5 mouse embryo
|
| Data processing |
The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.
|
| |
|
| Submission date |
Apr 28, 2009 |
| Last update date |
Nov 18, 2010 |
| Contact name |
Xing Li |
| Phone |
734-647-0171
|
| URL |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=17299133&dopt=Abstract
|
| Organization name |
Universtiy of Michigan
|
| Department |
Bioinformatics Program & CDB
|
| Lab |
Dr. Gumucio Lab
|
| Street address |
109 Zina Pitcher Place,045 BSRB
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109-2200 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE15872 |
Dynamic patterning at the pylorus: formation of an epithelial intestine-stomach boundary in late fetal life |
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