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Sample GSM160072 Query DataSets for GSM160072
Status Public on Jul 19, 2007
Title basal culture, 9A1, rep 2
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 1125.021611
1415671_at 633.1388003
1415672_at 2786.642085
1415673_at 558.761574
1415674_a_at 924.0717087
1415675_at 821.0048873
1415676_a_at 3465.260271
1415677_at 351.5039277
1415678_at 1750.568742
1415679_at 1592.77857
1415680_at 1671.132025
1415681_at 1086.672882
1415682_at 619.4813331
1415683_at 3173.182979
1415684_at 289.6058631
1415685_at 304.310436
1415686_at 958.0890873
1415687_a_at 2075.000545
1415688_at 1820.113875
1415689_s_at 668.5144804

Total number of rows: 22690

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM160072.CEL.gz 3.6 Mb (ftp)(http) CEL

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