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Sample GSM160440 Query DataSets for GSM160440
Status Public on Jul 19, 2007
Title D5 aggregate culture, 9A1, rep 1 (430)
Sample type RNA
 
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.
 
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 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.
 
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 10.89187516
1415671_at 11.19088771
1415672_at 12.17440946
1415673_at 8.666011439
1415674_a_at 10.34942373
1415675_at 9.748976461
1415676_a_at 11.77890582
1415677_at 11.62932942
1415678_at 11.23896726
1415679_at 11.7781366
1415680_at 9.441058731
1415681_at 10.80149695
1415682_at 9.011852298
1415683_at 11.16933982
1415684_at 10.02937724
1415685_at 9.502372835
1415686_at 10.54563282
1415687_a_at 11.94560507
1415688_at 11.37676353
1415689_s_at 9.775591271

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM160440.CEL.gz 3.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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