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Sample GSM161108 Query DataSets for GSM161108
Status Public on Feb 09, 2007
Title baseline sample at T0, rep1
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 105.266
AFFX-BioB-M_at 138.107
AFFX-BioB-3_at 144.782
AFFX-BioC-5_at 297.685
AFFX-BioC-3_at 291.4
AFFX-BioDn-5_at 656.381
AFFX-BioDn-3_at 860.112
AFFX-CreX-5_at 1798.72
AFFX-CreX-3_at 1788.4
AFFX-DapX-5_at 40.768
AFFX-DapX-M_at 42.3716
AFFX-DapX-3_at 17.6322
AFFX-LysX-5_at 18.6859
AFFX-LysX-M_at 38.4373
AFFX-LysX-3_at 156.771
AFFX-PheX-5_at 58.9666
AFFX-PheX-M_at 367.407
AFFX-PheX-3_at 111.175
AFFX-ThrX-5_at 118.284
AFFX-ThrX-M_at 22.6823

Total number of rows: 45101

Table truncated, full table size 851 Kbytes.




Supplementary file Size Download File type/resource
GSM161108.CEL.gz 3.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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