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Sample GSM353866 Query DataSets for GSM353866
Status Public on Dec 25, 2008
Title ratbladder_SCI_25d
Sample type RNA
 
Source name urinary bladder muscle post-spinal cord injury (25 days)
Organism Rattus norvegicus
Characteristics strain: Sprague Dawley
gender: female ,
age/weight: 170g
animal protocol:
An PE-10 intrathecal catheter (Clay-Adams, Parsippany, New Jersey) was implanted at the level of the L6 to S1 spinal cord after laminectomy at the Th11 vertebra with the rat under halothane anesthesia. The end of the catheter was heat sealed and placed subcutaneously. At 3 to 4 days after intrathecal catheter implantation spinal cord transection was performed between Th9 to Th10 with the rat under halothane anesthesia. After T9 laminectomy the dura and spinal cord were cut with scissors and a sterile Gelform sponge (The Upjohn Co., Kalamazoo, Michigan) was placed between the cut ends of the spinal cord. The overlying muscle and skin were sutured. Postoperatively the animals were treated with antibiotics (ampicillin, 150 mg./kg. intramuscularly) for 7 days. The bladder of spinalized rats was manually emptied twice daily until reflex voiding recovered, 14 days after spinalization.
tissues: urinary bladder muscle
Biomaterial provider Hilltop Labs
Treatment protocol bladder harvested under halothane anesthesia 25 days post-spinalization;
muscle layer dissected and snap-frozen in liquid nitrogen.
Growth protocol No specific protocol. Normal animal keeping, specific for spinalized animals, under DLAR protocol.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol reagent, and purified with Qiagen RNeasy kit
Label biotin
Label protocol The purified cDNA were incubated at 37 degC for 4 h in an in vitro transcription reaction to produce cRNA labeled with biotin using MEGAscriptTM system (Ambion, Inc., Austin, TX).
 
Hybridization protocol Fifteen to twenty micrograms of cRNA were fragmented by incubating in a buffer containing 200mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc at 958C for 35 min. The fragmented cRNAs were then hybridized with a pre-equilibrated Affymetrix chip at 458C for 14–16 h. After the hybridization cocktails were removed, the chips were then washed in a fluidic station with low-stringency buffer (6x SSPE, 0.01% Tween-20, 0.005% antifoam) for 10 cycles (2 mixes/cycle) and stringent buffer (100 mM MES, 0.1 M NaCl, and 0.01% Tween-20) for 4 cycles (15 mixes/cycle), and stained with SAPE (Strepto-avidin Phycoerythrin). This was followed by incubation with biotinylated mouse anti-avidin antibody, and restained with SAPE.
Scan protocol Affymetrix HP ChipScanner (G-7 scanner).
Software: GCOS1.4
Description ratbladder_SCI_25d
Data processing GCOS1.4, normalized through scaled target intensity.
 
Submission date Dec 22, 2008
Last update date Dec 24, 2008
Contact name Silvia Wognum
Organization name University of Pittsburgh
Department Bioengineering
Lab ETM2L
Street address 100 Technology Drive
City Pittsburgh
State/province PA
ZIP/Postal code 15219
Country USA
 
Platform ID GPL85
Series (1)
GSE14096 Urinary bladder post-spinal cord injury: time-points

Data table header descriptions
ID_REF
VALUE GCOS1.4, normalized through scaled target intensity
ABS_CALL absent or present
DETECTION P-VALUE detection p-value

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-MurIL2_at 26.5024 A 0.783476
AFFX-MurIL10_at 20.4581 A 0.814869
AFFX-MurIL4_at 3.39659 A 0.993129
AFFX-MurFAS_at 16.1378 A 0.868639
AFFX-BioB-5_at 669.2 P 0.0151826
AFFX-BioB-M_at 1846.61 P 0.000340305
AFFX-BioB-3_at 674.55 P 0.000662269
AFFX-BioC-5_at 1903.99 P 9.4506e-05
AFFX-BioC-3_at 1738.13 P 8.14279e-05
AFFX-BioDn-5_at 1439.2 P 0.000146581
AFFX-BioDn-3_at 9176.03 P 4.42873e-05
AFFX-CreX-5_at 22040.2 P 4.42873e-05
AFFX-CreX-3_at 31561.3 P 4.42873e-05
AFFX-BioB-5_st 186.805 A 0.147939
AFFX-BioB-M_st 173.644 A 0.41138
AFFX-BioB-3_st 51.9507 A 0.772364
AFFX-BioC-5_st 39.793 A 0.883887
AFFX-BioC-3_st 10.5977 A 0.749204
AFFX-BioDn-5_st 263.766 A 0.139482
AFFX-BioDn-3_st 328.202 P 0.0182806

Total number of rows: 8799

Table truncated, full table size 282 Kbytes.




Supplementary file Size Download File type/resource
GSM353866.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM353866.CHP.gz 2.9 Mb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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