NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM160071 Query DataSets for GSM160071
Status Public on Jul 19, 2007
Title basal culture, 9A1, rep 1
Sample type RNA
 
Source name bipotential mouse embryonic liver cell line 9A1, basal culture
Organism Mus musculus
Characteristics Strain: CBA/J x C57Bl/6J
Tissue: cell lines derived from dpc14 embryonic mouse liver
Cell line: 9A1
Culture condition : basal
Biomaterial provider M. Weiss lab at the Institut Pasteur, Paris, France.
Treatment protocol basal 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 basal 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.

Data table header descriptions
ID_REF
VALUE RMA-calculated Signal intensity

Data table
ID_REF VALUE
1415670_at 1066.892424
1415671_at 822.9106591
1415672_at 2724.156742
1415673_at 537.9588459
1415674_a_at 1011.175011
1415675_at 836.384201
1415676_a_at 3759.335608
1415677_at 361.2791032
1415678_at 1985.624354
1415679_at 1457.28466
1415680_at 1735.973248
1415681_at 1236.66412
1415682_at 778.4254131
1415683_at 3582.450363
1415684_at 394.0833536
1415685_at 323.8145496
1415686_at 1110.00003
1415687_a_at 1880.20858
1415688_at 1904.886072
1415689_s_at 684.2046032

Total number of rows: 22690

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM160071.CEL.gz 3.6 Mb (ftp)(http) CEL

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