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Status |
Public on Feb 02, 2016 |
Title |
FinHER_tumor_her2pos_117 |
Sample type |
RNA |
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|
Source name |
breast tumor
|
Organism |
Homo sapiens |
Characteristics |
tissue: breast tumor Sex: female batch: 3
|
Extracted molecule |
total RNA |
Extraction protocol |
mRNA extraction was performed using ZYMO research pinpoint slide RNA isolation system II. Pinpoint solution was added ro the tissue on a glass slide. After air-dry, a thin blue film that embeds the tissue underneath is formed. This was then lifted from the slide and transferred to a tube. Following the treatment of the tissue with Proteinase K and RNA digestions and extraction buffers, the extracted RNA was washed and concentered using the Zymo-Spin TM IC Column
|
Label |
biotin
|
Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
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|
|
Hybridization protocol |
Following fragmentation, 132 ng of cRNA were hybridized overnight at 45C on HG U219 96-array plate.
|
Scan protocol |
GeneChips were scanned using the GeneChip Scanner by Affymetrix.
|
Data processing |
The data were analyzed with R-Bioconductor statistical suite. Data were normalized using the RMA function (affy package) and a batch effect correction was applied via the ComBat function of the sva package.
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|
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Submission date |
Jan 20, 2015 |
Last update date |
Mar 01, 2023 |
Contact name |
Christos Sotiriou |
E-mail(s) |
christos.sotiriou@hubruxelles.be
|
Phone |
+32 2 541 34 57
|
Organization name |
Institut Jules Bordet – Université Libre de Bruxelles (ULB)
|
Lab |
Breast Cancer Translational Research Laboratory J.C. Heuson (ULB 290)
|
Street address |
Rue Meylemeersch 90
|
City |
Brussels |
ZIP/Postal code |
1070 |
Country |
Belgium |
|
|
Platform ID |
GPL13667 |
Series (1) |
GSE65095 |
FinHER trial : Patients with human epidermal growth factor receptor 2 (HER2)–positive breast cancer |
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