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Status |
Public on Jul 19, 2007 |
Title |
D5 aggregate culture, 9A1, rep 1 (430) |
Sample type |
RNA |
|
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Source name |
bipotential mouse embryonic liver cell line 9A1, aggregate culture 5 days
|
Organism |
Mus musculus |
Characteristics |
Strain: embryos were derived from a CBA/J x C57Bl/6J cross. Tissue: cell lines derived from dpc14 embryonic mouse liver Cell line: 9A1 Culture condition : aggregate 5 days
|
Biomaterial provider |
GJ Darlington lab at Baylor College of Medicine, Houston, Texas, USA.
|
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.
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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).
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Description |
Gene expression data from 9A1 BMEL cells cultured 5 days 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.
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Submission date |
Feb 05, 2007 |
Last update date |
Aug 28, 2018 |
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 |
|
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Platform ID |
GPL1261 |
Series (2) |
GSE6957 |
Transcriptional profiling of bipotential embryonic liver cells to identify liver progenitor cell surface markers (430) |
GSE6966 |
Transcriptional profiling of bipotential embryonic liver cells to identify liver progenitor cell surface markers. |
|
Relations |
Reanalyzed by |
GSE119085 |