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Sample GSM1565763 Query DataSets for GSM1565763
Status Public on Jul 01, 2019
Title A/J, one-week, vehicle treated, biological rep4
Sample type RNA
 
Source name A/J_1-week 0.9% NaCl treated_drosal root ganglia
Organism Mus musculus
Characteristics strain: A/J
gender: female
age: 9 weeks
treated with: 0.9% NaCl
timepoint: 1-week
tissue: L4-L5 dorsal root ganglia
Treatment protocol No treatment, 4mg/kg cisplatin, or 0.9% NaCl were admissistered twice weekly over the specified time period.
Growth protocol Adult female C57BL6/J and A/J (20–30 g; The Jackson Laboratory, Bar Harbor, ME) mice were used for the study. All mice were housed on a 12:12 h light/dark cycle with food and water available ad libitum. All experiments were approved by the institutional animal care and use committee of the University of Maryland School of Medicine, and conducted in accordance with The International Association for the Study of Pain guidelines for investigations of pain in animals. On each experimental day, the mice were weighed to detect changes in food and water consumption. Any mouse that demonstrated signs of debilitation or weight loss > 10% vs. baseline was euthanized.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 100 ng of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the AffyMetrix GeneChip Scanner 3000 7G.
Description Gene expression data from drosal root ganglia of vehicle treated A/J mice after one-week
AJ_DRG_VEHICLE_1wk_4
Data processing The data were analyzed using the R software suite. Array intensities were normalized with the robust multichip average method and probe set to gene mapping was done using the BrainArray Custom CDF version 18 (Dai, M. et al., Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 33 (20), 175 (2005)). Batch effect correction was performed using nonparametric empirical Bayes methods as implemented in ComBat with naive samples serving as covariates (Johnson, W., Rabinovic, A. & Li, C., Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8 (1), 118-127 (2007)).
RMA, BrainArray Custom CDF version 18
 
Submission date Dec 15, 2014
Last update date Jul 01, 2019
Contact name Susan G Dorsey
E-mail(s) sdorsey@son.umaryland.edu
Phone (410) 706-7250
Organization name University Of Maryland, Baltimore
Department University of Maryland School of Nursing
Lab Center for the Advancement of Chronic Pain Research
Street address 655 W. Lombard Street, Room 727A
City Baltimore
State/province MD
ZIP/Postal code 21201
Country USA
 
Platform ID GPL19559
Series (1)
GSE64174 Expression Data for Cisplatin Treated Dorsal Root Ganglia from A/J and C57BL/6J Mice

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
100008567_at 6.329680819
100009600_at 5.524884031
100012_at 3.161149496
100017_at 5.326117709
100019_at 7.625777881
100034251_at 7.860084156
100034739_at 4.438605817
100034748_at 4.300797883
100036520_at 4.240165466
100036521_at 8.685376114
100036523_at 4.544300387
100036768_at 4.129947092
100037258_at 8.638818218
100037262_at 5.113690306
100037278_at 5.64812888
100038347_at 6.938145346
100038358_at 4.692452171
100038371_at 4.002471125
100038392_at 4.151930537
100038398_at 4.904636507

Total number of rows: 17543

Table truncated, full table size 364 Kbytes.




Supplementary file Size Download File type/resource
GSM1565763_Mouse430-18-Veh2B-AJ_1wk.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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