NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM189094 Query DataSets for GSM189094
Status Public on Oct 23, 2008
Title Kidney_400 mg/kg VCM ip_mouse #107
Sample type RNA
 
Source name Kidney from mice treated with 7 daily ip injections of vancomycin at 400 mg/kg
Organism Mus musculus
Characteristics tissue: kidney
protocol: intraperitoneal
agent: vancomycin
dose: 400 mg/kg
Treatment protocol Groups of 6 mice were administered, daily for 7 consecutive days, with 50, 200, and 400 mg/kg vancomycin, delivered via the iv and ip routes. Six control mice were administered a similar volume of 0.9% saline solution using both routes.
Growth protocol BALB/c mice were maintained on Purina Certified Rodent Chow 5002 (Richmond, IN, USA) and purified tap water ad libitum in microisolator cages under controlled lighting (12 h light/dark cycle).
Extracted molecule total RNA
Extraction protocol Approximately 15-20 mg of each kidney to analyze was transferred into 1 ml Trizol reagent (Invitrogen, Carlsbad, CA, USA) along with a stainless steel bead (Qiagen, Valencia, CA, USA) and homogenized with a TissueLyser (Qiagen). Total RNA was extracted with 200 µl chloroform, precipitated with 500 µl 100% ethanol, and transferred to a RNeasy mini spin column (Qiagen) for purification according to the manufacturer’s instructions. Total RNA was subsequently precipitated with ethanol, resuspended in water and stored at –70°C.
Label Biotin
Label protocol cDNA was prepared and cleaned from 10 µg total RNA using the One-Cycle cDNA Synthesis and Clean-up module kits (Affymetrix, Santa Clara, CA, USA). The cDNA was further processed to biotin-labeled cRNA using the IVT labeling kit (Affymetrix). Labeling protocol was performed according to the manufacturer’s instructions, as described in the Affymetrix Genechip Expression Analysis Technical Manual, revision 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
 
Hybridization protocol The cRNA was fragmented before hybridizing to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Hybridization was performed according to the manufacturer’s instructions, as described in the Affymetrix Genechip Expression Analysis Technical Manual, revision 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
Scan protocol Scaning was performed using a TGT value = 500 using the protocol described in the Affymetrix Genechip Expression Analysis Technical Manual, revision 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)
Description Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 400 mg/kg administered via the intraperitoneal route (ip)
Data processing The Affymetrix CEL files were loaded into GeneSpring GX version 7.3.1 (Agilent technologies, Santa Clara, CA, USA) and preprocessed using GenChip Robust Multi-Array analysis (GC-RMA).
 
Submission date May 14, 2007
Last update date Aug 28, 2018
Contact name Hanna Hongchin Ng
E-mail(s) hanna.ng@sri.com
Organization name SRI International
Street address 333 Ravenswood Avenue
City Menlo Park
State/province CA
ZIP/Postal code 94025
Country USA
 
Platform ID GPL1261
Series (1)
GSE7793 Vancomycin nephrotoxicity assessed by DNA microarray
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 870.199 P 0.000581214
AFFX-BioB-M_at 1720.2 P 4.42873e-05
AFFX-BioB-3_at 1750.77 P 4.42873e-05
AFFX-BioC-5_at 493.082 P 6.02111e-05
AFFX-BioC-3_at 638.343 P 4.42873e-05
AFFX-BioDn-5_at 349.165 P 4.42873e-05
AFFX-BioDn-3_at 2985.32 P 4.42873e-05
AFFX-CreX-5_at 1379.32 P 5.16732e-05
AFFX-CreX-3_at 687.322 P 4.42873e-05
AFFX-DapX-5_at 2620.1 P 4.42873e-05
AFFX-DapX-M_at 549.301 P 5.16732e-05
AFFX-DapX-3_at 792.152 P 4.42873e-05
AFFX-LysX-5_at 155.584 P 5.16732e-05
AFFX-LysX-M_at 1197.85 P 9.4506e-05
AFFX-LysX-3_at 287.162 P 5.16732e-05
AFFX-PheX-5_at 380.219 P 4.42873e-05
AFFX-PheX-M_at 775.284 P 5.16732e-05
AFFX-PheX-3_at 7184.7 P 4.42873e-05
AFFX-ThrX-5_at 1062.46 P 6.02111e-05
AFFX-ThrX-M_at 180.175 P 4.42873e-05

Total number of rows: 45101

Table truncated, full table size 1387 Kbytes.




Supplementary file Size Download File type/resource
GSM189094.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM189094.CHP.gz 244.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap