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Sample GSM493244 Query DataSets for GSM493244
Status Public on Dec 07, 2010
Title Hydroxyapatite-coated cellulose, 3 days, rat 7
Sample type RNA
 
Source name subcutaneous implantation of hydroxyapatite-coated cellulose, 3 days, rat 7
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
age: 10 weeks
tissue: Granulation tissue
time: 3 days
Growth protocol Subcutaneous implantation into rat
Extracted molecule total RNA
Extraction protocol Total RNA from implants was isolated with RNeasy midi kit according to manufacturer´s instructions, followed by the Dnase I treatment (Promega) as recommended by manufacturer.
Label biotin
Label protocol For the Illumina gene expression analysis, 100 ng of purified total RNA was amplified and biotinylated in an overnight in vitro transcription reaction using the Illumina RNA TotalPrepTM amplification kit (Ambion, Applied Biosystems).
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description no additional information
Data processing The data were normalized using quantile normalisation with limma in R
 
Submission date Jan 05, 2010
Last update date Dec 07, 2010
Contact name Miretta Tommila
E-mail(s) miorli@utu.fi
Organization name Turun yliopisto
Department Lääketieteellisen biokemian ja genetiikan laitos
Street address Kiinamyllynkatu 10
City Turku
ZIP/Postal code 20520
Country Finland
 
Platform ID GPL6101
Series (1)
GSE19748 Gene expression screening during early granulation tissue formation (I)

Data table header descriptions
ID_REF
VALUE quantile normalized signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2039396 3535.640833 0
ILMN_2040732 133.06415 0.006060606
ILMN_2039699 137.350825 0.004848485
ILMN_2038916 130.41905 0.006060606
ILMN_1374916 8658.018667 0
ILMN_1353986 89.22532583 0.350303
ILMN_1366832 108.5708175 0.03030303
ILMN_1366017 91.65923417 0.2787879
ILMN_1354115 135.2445917 0.006060606
ILMN_1356225 87.49963667 0.4193939
ILMN_1373889 94.86503167 0.2
ILMN_1372047 344.6407333 0
ILMN_1372803 90.50077917 0.3066667
ILMN_1369380 71.1794175 0.9709091
ILMN_1366418 152.88365 0.003636364
ILMN_1349281 905.40755 0
ILMN_1354519 87.371665 0.4230303
ILMN_1363384 210.4921917 0.002424242
ILMN_1373604 86.15661583 0.4630303
ILMN_1356361 539.4306917 0

Total number of rows: 22517

Table truncated, full table size 717 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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