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Sample GSM258401 Query DataSets for GSM258401
Status Public on Mar 31, 2008
Title Sham brain set B
Sample type RNA
 
Source name Rat whole brain
Organism Rattus norvegicus
Characteristics rats from five experimental groups were sacrificed 19–21 days after surgery
Treatment protocol Rats having the L5-L6 spinal nerves ligated (SNL) were performed, Sham-operation consisted of exposing the spinal nerves without ligation or manipulation. Naïve animals did not receive surgery.Rats were tested before and 12–14 days after surgery. Only SNL rats exhibiting a significantly reduced PWT in the ipsilateral limb were included in drug testing or gene expression studies (eight to twelve rats per group). Vehicle (0.9% saline) or gabapentin (GPN; 100 mg/kg dissolved in 0.9% saline) was administered intraperitoneally (i.p.) once a day for 7 days in a volume of 2 ml/kg. On the last (7th) treatment day (corresponding to 19–21 days post-surgery), rats were again assessed by PWT, in particular to confirm the reversal of neuropathic pain with GPN treatment.
Growth protocol For gene expression analysis, rats from five experimental groups were sacrificed 19–21 days after surgery
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 (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 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
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
 
Submission date Jan 22, 2008
Last update date Jan 22, 2008
Contact name Jason Gang Jin
E-mail(s) jasongjin@gmail.com
Phone 732-220-9988
Fax 732-960-2355
Organization name MaxyBio
Street address 675 US Highway
City North Brunswick
ZIP/Postal code 08902
Country USA
 
Platform ID GPL86
Series (1)
GSE10238 Complement activation in the peripheral nervous system following the spinal nerve ligation model of neuropathic pain

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX_rat_5S_rRNA_at 37.4 A 0.156732
AFFX_Rat_beta-actin_3_at 1845.7 P 0.000052
AFFX_Rat_beta-actin_3_st 14.5 A 0.5
AFFX_Rat_beta-actin_5_at 1078.2 P 0.000052
AFFX_Rat_beta-actin_5_st 2.4 A 0.997725
AFFX_Rat_beta-actin_M_at 1669.3 P 0.000052
AFFX_Rat_beta-actin_M_st 8.7 A 0.51489
AFFX_Rat_GAPDH_3_at 2209.4 P 0.000662
AFFX_Rat_GAPDH_3_st 15.3 P 0.002275
AFFX_Rat_GAPDH_5_at 1841.6 P 0.000044
AFFX_Rat_GAPDH_5_st 17.2 A 0.262827
AFFX_Rat_GAPDH_M_at 1973.9 P 0.000044
AFFX_Rat_GAPDH_M_st 31.5 A 0.340661
AFFX_Rat_Hexokinase_3_at 159 P 0.000052
AFFX_Rat_Hexokinase_5_at 90.3 P 0.000095
AFFX_Rat_Hexokinase_M_at 162 P 0.011384
AFFX_ratb1/X12957_at 40.9 P 0.00762
AFFX_ratb2/X14115_at 14.8 A 0.165861
AFFX-BioB-3_at 168.6 P 0.000225
AFFX-BioB-3_st 4.1 A 0.860518

Total number of rows: 8791

Table truncated, full table size 263 Kbytes.




Supplementary file Size Download File type/resource
GSM258401.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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