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Sample GSM160078 Query DataSets for GSM160078
Status Public on Jul 19, 2007
Title D5 aggregate culture, 14B3, rep 2
Sample type RNA
 
Source name bipotential mouse embryonic liver cell line 14B3, aggregate culture 5 days
Organism Mus musculus
Characteristics Strain: CBA/J x C57Bl/6J
Tissue: cell lines derived from dpc14 embryonic mouse liver
Cell line: 14B3
Culture condition : aggregate
Biomaterial provider M. Weiss lab at the Institut Pasteur, Paris, France.
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 14B3 BMEL cells cultured 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 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 979.4153522
1415671_at 1494.495668
1415672_at 2752.170244
1415673_at 270.8687219
1415674_a_at 1039.125363
1415675_at 1058.564894
1415676_a_at 3028.790341
1415677_at 1829.241703
1415678_at 2001.534822
1415679_at 1951.949482
1415680_at 922.3790914
1415681_at 1372.404456
1415682_at 562.2422267
1415683_at 2589.588233
1415684_at 434.6312205
1415685_at 298.7351109
1415686_at 1108.684378
1415687_a_at 2241.293704
1415688_at 1791.924329
1415689_s_at 770.1315017

Total number of rows: 22690

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM160078.CEL.gz 2.2 Mb (ftp)(http) CEL

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