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Sample GSM729525 Query DataSets for GSM729525
Status Public on Jan 01, 2012
Title Tube alone (K), caudal to the lesion (C), 1 day post-op, biol rep1
Sample type RNA
 
Source name 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 1 day after operation
Organism Rattus norvegicus
Characteristics tissue: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord
treatment: spinal cord injury and tube control treatment
time: 1 day after operation
strain: Wistar rat
gender: female
age: adult rat, i.e. 2 months after birth
Treatment protocol Wistar rats weighing 250-300 g each were anaesthetized , followed by transection at the T7-8 level removing a spinal cord segment 5.0 mm in length. The blade was repeatedly scraped along the ventral surface of the spinal canal, and any residual fibers at the lesion site were removed by aspiration. The animals were divided into 3 groups. One group (NT-3-chitosan tube) received a chitosan tube of 5 mm in length, with a 2.2 mm outer diameter and 2.0 mm in inner diameter, seeded with the NT-3-chitosan carriers, implanted into the lesioned area. A second group (tube alone) had implanted only an empty chitosan tube. A third group (lesion control) received no treatment after the operation.
Growth protocol The experimental rats were kept at a temperature of 24-26ºC, and humidity of 35-45% with twelve h light-dark cycles. Food and water were provided ad libitum. Supplemental oral feedings were given as necessary.
Extracted molecule total RNA
Extraction protocol The samples for microarray analysis were homogenized in 1 ml Trizol (Invitrogen, Carlsbad, CA), and RNA extracted using RNEasy miniprep columns (Qiagen, Valencia, CA) according to the manufacturer’s instructions. An average of 40-60 ug RNA was obtained from 80-120 mg of tissue pooled from four animals for microarray analysis which was performed using an Affymetrix GeneChipÒ Rat Genome 230 2.0 chip for each time point. All assays were performed at least in triplicate biological independent pooled samples.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.
Description Gene expression data from adult rat of tube alone treatment
Data processing The data were analyzed with Expression Console Software using RMA algorithm.
 
Submission date May 23, 2011
Last update date Jan 01, 2012
Contact name Li Xiaoguang
E-mail(s) lxgchina@sina.com
Phone 086101083911570
Fax 086101083911570
Organization name Beihang University
Department School of Biological Science and Medical Engineering
Lab Neural and Tissue Engineering Lab
Street address No.37 of Xueyuan Road, Haidian District
City Beijing
ZIP/Postal code 100191
Country China
 
Platform ID GPL1355
Series (1)
GSE29488 Patterns of gene Expression during the Spinal cord Injury/Regeneration

Data table header descriptions
ID_REF
VALUE log2 GC-RMA signal

Data table
ID_REF VALUE
AFFX-BioB-5_at 8.98
AFFX-BioB-M_at 9.73
AFFX-BioB-3_at 9.46
AFFX-BioC-5_at 10.39
AFFX-BioC-3_at 10.76
AFFX-BioDn-5_at 11.56
AFFX-BioDn-3_at 12.98
AFFX-CreX-5_at 14.01
AFFX-CreX-3_at 14.29
AFFX-DapX-5_at 9.97
AFFX-DapX-M_at 10.66
AFFX-DapX-3_at 11.32
AFFX-LysX-5_at 6.68
AFFX-LysX-M_at 7.27
AFFX-LysX-3_at 8.44
AFFX-PheX-5_at 8
AFFX-PheX-M_at 7.88
AFFX-PheX-3_at 8.43
AFFX-ThrX-5_at 8.25
AFFX-ThrX-M_at 8.51

Total number of rows: 31099

Table truncated, full table size 489 Kbytes.




Supplementary file Size Download File type/resource
GSM729525_090929-Rat230_2-09266C_kC1_1d.CEL.gz 2.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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