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Sample GSM161109 Query DataSets for GSM161109
Status Public on Feb 09, 2007
Title baseline sample at T0, rep2
Sample type RNA
 
Source name 10-week-old normal female liver sample
Organism Mus musculus
Characteristics Genotype: Female CD-1 mouse
Age: 10 week
Treatment protocol After anesthesia with 100 mg/kg ketamine and 10 mg/kg Xylazine, the abdomen was prepped with alcohol and betadyne. Aftermidline laparotomy, the tip of the xiphoid was resected, and the liver exteriorized. A silk tie was placed around the three anterior lobes of the liver, including the gallbladder, and the 2/3 hepatectomy with cholecystectomy was completed. The liver was returned to the abdominal cavity and the abdomen closed in two layers. Postoperative analgesia consisted of Buprenorphine 0.05-0.1 mg/kg twice daily for 48 hours or until sacrifice. At harvest,mice were sacrificed with carbon dioxide asphyxiation followed by cervical dislocation.
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.
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 117.976
AFFX-BioB-M_at 155.988
AFFX-BioB-3_at 164.032
AFFX-BioC-5_at 364.659
AFFX-BioC-3_at 332.166
AFFX-BioDn-5_at 846.511
AFFX-BioDn-3_at 1687.54
AFFX-CreX-5_at 4291.57
AFFX-CreX-3_at 4714.53
AFFX-DapX-5_at 65.1313
AFFX-DapX-M_at 42.9978
AFFX-DapX-3_at 16.0242
AFFX-LysX-5_at 16.3578
AFFX-LysX-M_at 58.2147
AFFX-LysX-3_at 94.3346
AFFX-PheX-5_at 78.1328
AFFX-PheX-M_at 176.918
AFFX-PheX-3_at 97.9151
AFFX-ThrX-5_at 130.759
AFFX-ThrX-M_at 28.2981

Total number of rows: 45101

Table truncated, full table size 851 Kbytes.




Supplementary file Size Download File type/resource
GSM161109.CEL.gz 3.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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