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Status |
Public on May 01, 2014 |
Title |
Clinical Breast Cancer Specimen from patient developing distant metastasis 659_dev.meta |
Sample type |
RNA |
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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
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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
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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.
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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 |
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