|
| Status |
Public on Jul 19, 2007 |
| Title |
D5 aggregate culture, 9A1, rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
bipotential mouse embryonic liver cell line 9A1, aggregate culture 5 days
|
| Organism |
Mus musculus |
| Characteristics |
Strain: CBA/J x C57Bl/6J
Tissue: cell lines derived from dpc14 embryonic mouse liver
Cell line: 9A1
Culture condition : aggregate
|
| Biomaterial provider |
M. Weiss lab at the Institut Pasteur, Paris, France.
|
| Treatment protocol |
aggregate culture (Strick-Marchand H, Weiss MC. Inducible differentiation and morphogenesis of bipotential liver cell lines from wild-type mouse embryos. Hepatology. 2002;36:794-804)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions. RNA had an 18S/28S ratio greater than 1.7, a 260/230 ratio greater than 1.5, and a lack of visual RNA degradation on Agilent 2100 Bioanalyzer electropherograms (Agilent Technologies Inc.).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Array 430a . GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (non-upgraded).
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 (non-upgraded).
|
| Description |
Gene expression data from 9A1 BMEL cells cultured under aggregate conditions.
|
| Data processing |
The data were analyzed with the Bioconductor affy (Gautier L, Cope L, Bolstad BM, et al. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (Oxford, England). 2004;20(3):307-315) package using R 2.3.1 and RMA (Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (Oxford, England). 2003;4(2):249-264) as the normalization method.
|
| |
|
| Submission date |
Feb 02, 2007 |
| Last update date |
Jul 11, 2007 |
| Contact name |
Scott Andrew Ochsner |
| E-mail(s) |
sochsner@bcm.edu
|
| Phone |
713-798-6227
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Cellular Biology
|
| Lab |
SPP: Signaling Pathways Project
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL339 |
| Series (2) |
| GSE6942 |
Transcriptional profiling of bipotential embryonic liver cells to identify liver progenitor cell surface markers (430A) |
| GSE6966 |
Transcriptional profiling of bipotential embryonic liver cells to identify liver progenitor cell surface markers. |
|
