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Sample GSM161135 Query DataSets for GSM161135
Status Public on Feb 09, 2007
Title developmental sample at T135, rep2
Sample type RNA
 
Source name Liver sample from mouse embryo liver at 13.5 days post conception (dpc)
Organism Mus musculus
Characteristics Genotype: CD-1 mouse embryo
Age: 10.5 dpc
Treatment protocol Pregnant CD-1 females were sacrificed with carbon dioxide asphyxiation followed by cervical dislocation. The abdomen was opened and the uterus removed. After removal of the uterine musculature, embryos were removed from the yolk sacs and livers microdissected, taking care to remove all extraneous tissue including the retrohepatic vena cava.
Growth protocol All experiments used CD-1 mice obtained from Charles River Laboratories (Wilmington, MA) or our own breeding colony. Animals were maintained in a pathogenfree facility administered by Harvard Medical School in accordance with the institutional guidelines of Harvard Medical School and Beth Israel Deaconess Medical Center. A maximum of five minutes was allowed to elapse between sacrifice and liver harvest to prevent RNA degradation and transcriptional changes.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Gene expression data from 10-week-old normal female liver sample.
Data processing The data were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied.
 
Submission date Feb 08, 2007
Last update date Aug 28, 2018
Contact name Hasan Huseyin Otu
E-mail(s) hotu@bidmc.harvard.edu
Organization name Harvard Medical School
Department Medicine
Lab BIDMC Genomics Center
Street address 4 Blackfan Circle Rm. 238
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL1261
Series (1)
GSE6998 Expression profiling of developmental and regenerating liver in mice
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF Affymetrix probe set id
VALUE dChip normalized modeled signal value

Data table
ID_REF VALUE
AFFX-BioB-5_at 127.504
AFFX-BioB-M_at 158.124
AFFX-BioB-3_at 188.879
AFFX-BioC-5_at 343.429
AFFX-BioC-3_at 316.162
AFFX-BioDn-5_at 910.832
AFFX-BioDn-3_at 1672.07
AFFX-CreX-5_at 3963.64
AFFX-CreX-3_at 4052.89
AFFX-DapX-5_at 28.665
AFFX-DapX-M_at 41.1468
AFFX-DapX-3_at 10.6381
AFFX-LysX-5_at 26.2916
AFFX-LysX-M_at 27.6956
AFFX-LysX-3_at 78.1965
AFFX-PheX-5_at 40.2938
AFFX-PheX-M_at 231.087
AFFX-PheX-3_at 82.4008
AFFX-ThrX-5_at -65.4556
AFFX-ThrX-M_at 20.2564

Total number of rows: 45101

Table truncated, full table size 851 Kbytes.




Supplementary file Size Download File type/resource
GSM161135.CEL.gz 6.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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