NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM160437 Query DataSets for GSM160437
Status Public on Jul 19, 2007
Title D1 aggregate culture, 9A1, rep 2 (430)
Sample type RNA
 
Source name bipotential mouse embryonic liver cell line 9A1, aggregate culture 1 day
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 1 day
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.
 
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 1 day 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 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
 
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

Data table header descriptions
ID_REF [required; this column should correspond to the ID column of the reference platform]
VALUE RMA-calculated Signal intensity

Data table
ID_REF VALUE
1415670_at 10.64818092
1415671_at 11.33391642
1415672_at 11.81837329
1415673_at 6.96198058
1415674_a_at 9.571398668
1415675_at 9.860576772
1415676_a_at 11.36132855
1415677_at 9.966128255
1415678_at 11.18196581
1415679_at 10.7654698
1415680_at 9.622276917
1415681_at 10.33323563
1415682_at 8.879392994
1415683_at 11.28898085
1415684_at 8.547994661
1415685_at 8.874772001
1415686_at 10.55002678
1415687_a_at 11.96443563
1415688_at 11.02276755
1415689_s_at 9.293768341

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM160437.CEL.gz 4.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap