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Sample GSM913183 Query DataSets for GSM913183
Status Public on May 01, 2014
Title Clinical Breast Cancer Specimen from patient developing distant metastasis 659_dev.meta
Sample type RNA
 
Source name Clinical Breast Cancer Specimen
Organism Homo sapiens
Characteristics distant metastasis (0-none): 1
dfs (months): 32
age (y): 78
tumor size: 2.3
histotype: CDI
esr1 status (0-negative): 1
erbb2 status (0-negative): 0
tissue: breast cancer specimen
Growth protocol Tissue samples collected at time of surgery were stored at -80°C until RNA extraction
Extracted molecule total RNA
Extraction protocol Tissue was pulverized using a Mikrodismembrator (Braun Biotech International , Germany). Total RNA was extracted with the Trizol reagent (Invitrogen, Carlsbad, CA) according to manufacture instructions and an additional DNase digestion was performed using the RNeasy kit (Qiagen, Valencia, CA).
Label biotin
Label protocol 800 ng of total RNA were reverse transcribed, labeled with biotin and amplified overnight using the Illumina RNA TotalPrep Amplification kit (Ambion, Austin, TX) according to manufacturer’s protocol
 
Hybridization protocol One μg of the biotinylated cRNA sample was mixed with the Hyb E1 hybridization buffer containing 37.5% (w/w) formamide and then hybridized at 58 °C overnight to the HumanRef-6_v3 (Illumina, Inc, San Diego, CA)
Scan protocol scanned with Illumina BeadArray Reader
Description Clinical Breast Cancer Specimen from patient developing distant metastasis
Data processing Microarray raw data where generated using the Illumina BeadStudio 3.8 software and processed using the lumi package of Bioconductor. After quality control, the Robust Spline Normalization was applied.
 
Submission date Apr 11, 2012
Last update date May 01, 2014
Contact name Maurizio Callari
E-mail(s) [email protected]
Organization name Fondazione IRCCS Istituto Nazionale dei Tumori
Street address Via Amadeo, 42
City Milan
ZIP/Postal code 20133
Country Italy
 
Platform ID GPL6884
Series (1)
GSE37181 Subtype-dependent prognostic relevance of an interferon-induced pathway metagene in human node negative breast cancer

Data table header descriptions
ID_REF
VALUE Log2 tranformation; Robust Spline Normalization
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1825594 6.748764938 0.93017
ILMN_1810803 7.300884842 0.22266
ILMN_1722532 10.06561593 0
ILMN_1884413 6.961687386 0.70487
ILMN_1906034 7.255822797 0.27404
ILMN_1861479 7.024691898 0.62055
ILMN_1708805 8.129820893 0.01713
ILMN_1874224 7.207936393 0.3307
ILMN_1672526 8.722224427 0.00791
ILMN_2185604 6.717372184 0.9473
ILMN_1785107 9.6287949 0
ILMN_1810805 9.900983263 0
ILMN_1689711 7.170762804 0.38208
ILMN_1782551 8.462301236 0.01318
ILMN_1820586 7.193677697 0.35441
ILMN_1838256 7.222063381 0.31884
ILMN_1901322 7.265076697 0.2635
ILMN_1715540 8.593434193 0.01054
ILMN_2371280 10.85889703 0
ILMN_1891455 9.779002905 0

Total number of rows: 48803

Table truncated, full table size 1498 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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