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Sample GSM1565755 Query DataSets for GSM1565755
Status Public on Jul 01, 2019
Title C57BL/6J, four-weeks, naive, biological rep2
Sample type RNA
 
Source name C57BL/6J_4-weeks untreated_drosal root ganglia
Organism Mus musculus
Characteristics strain: C57BL/6J
gender: female
age: 12 weeks
treated with: none (untreated control)
timepoint: 4-weeks
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 untreated C57BL/6J mice after four-weeks
C57BL6_DRG_NAIVE_4wk_2
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 6.346847296
100009600_at 5.239619206
100012_at 3.276952401
100017_at 4.983223666
100019_at 7.983347167
100034251_at 7.397386785
100034739_at 4.152641251
100034748_at 4.214629667
100036520_at 3.755681173
100036521_at 8.312129818
100036523_at 4.189013628
100036768_at 4.564803092
100037258_at 8.879054506
100037262_at 4.837129085
100037278_at 5.235189059
100038347_at 7.323439742
100038358_at 4.696850419
100038371_at 4.080859063
100038392_at 4.120574709
100038398_at 4.157607426

Total number of rows: 17543

Table truncated, full table size 364 Kbytes.




Supplementary file Size Download File type/resource
GSM1565755_Dorsey-Mouse430-R2_180_C57BL_DRG_NAIVE_4wk.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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