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Status |
Public on Jan 01, 2012 |
Title |
NT-3-chitosan tube (S), caudal to the lesion (C), 3 days post-op, biol rep3 |
Sample type |
RNA |
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Source name |
5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 3 days after operation
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Organism |
Rattus norvegicus |
Characteristics |
tissue: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord treatment: spinal cord injury and NT-3-chitosan tube treatment time: 3 days after operation strain: Wistar rat gender: female age: adult rat, i.e. 2 months after birth
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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.
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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.
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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.
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Label |
biotin
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Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, Affymetrix).
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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.
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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.
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Description |
Gene expression data from adult rat of NT-3-chitosan tube treatment
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Data processing |
The data were analyzed with Expression Console Software using RMA algorithm.
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Submission date |
May 23, 2011 |
Last update date |
Jan 01, 2012 |
Contact name |
Li Xiaoguang |
E-mail(s) |
lxgchina@sina.com
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Phone |
086101083911570
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Fax |
086101083911570
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Organization name |
Beihang University
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Department |
School of Biological Science and Medical Engineering
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Lab |
Neural and Tissue Engineering Lab
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Street address |
No.37 of Xueyuan Road, Haidian District
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City |
Beijing |
ZIP/Postal code |
100191 |
Country |
China |
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Platform ID |
GPL1355 |
Series (1) |
GSE29488 |
Patterns of gene Expression during the Spinal cord Injury/Regeneration |
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