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Sample GSM353862 Query DataSets for GSM353862
Status Public on Dec 25, 2008
Title ratbladder_normalcontrol
Sample type RNA
Source name urinary bladder muscle healthy (normal control)
Organism Rattus norvegicus
Characteristics strain: Sprague Dawley
gender: female
age/weight: 170g
tissues: urinary bladder muscle
Biomaterial provider Hilltop Labs
Treatment protocol bladder harvested under halothane anesthesia;
muscle layer dissected and snap-frozen in liquid nitrogen.
Growth protocol No specific protocol. Normal animal keeping 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_normalcontrol
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
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
VALUE GCOS1.4, normalized through scaled target intensity
ABS_CALL absent or present
DETECTION P-VALUE detection p-value

Data table
AFFX-MurIL2_at 40.4369 A 0.804734
AFFX-MurIL10_at 23.2171 A 0.760937
AFFX-MurIL4_at 5.39827 A 0.9273
AFFX-MurFAS_at 12.7041 A 0.876428
AFFX-BioB-5_at 574.327 M 0.0542134
AFFX-BioB-M_at 1101.06 P 0.0032123
AFFX-BioB-3_at 280.887 P 0.036569
AFFX-BioC-5_at 1359.84 P 0.000509415
AFFX-BioC-3_at 898.307 P 0.00159257
AFFX-BioDn-5_at 948.977 P 0.000753643
AFFX-BioDn-3_at 8258.04 P 0.00010954
AFFX-CreX-5_at 12095.3 P 4.42873e-05
AFFX-CreX-3_at 20014 P 4.42873e-05
AFFX-BioB-5_st 180.715 A 0.123572
AFFX-BioB-M_st 88.7761 A 0.559354
AFFX-BioB-3_st 49.9607 A 0.824672
AFFX-BioC-5_st 36.7219 A 0.941556
AFFX-BioC-3_st 17.5038 A 0.910522
AFFX-BioDn-5_st 254.484 A 0.147939
AFFX-BioDn-3_st 440.989 P 0.036569

Total number of rows: 8799

Table truncated, full table size 281 Kbytes.

Supplementary file Size Download File type/resource
GSM353862.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM353862.CHP.gz 2.7 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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