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Sample GSM1587047 Query DataSets for GSM1587047
Status Public on Feb 02, 2016
Title FinHER_tumor_her2pos_13
Sample type RNA
 
Source name breast tumor
Organism Homo sapiens
Characteristics tissue: breast tumor
Sex: female
batch: 1
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).
 
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.
 
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

Data table header descriptions
ID_REF
VALUE RMA log2 intensity

Data table
ID_REF VALUE
11715100_at 7.98791608
11715101_s_at 4.396037365
11715102_x_at 7.308032647
11715103_x_at 7.697007628
11715104_s_at 5.609957905
11715105_at 1.995803588
11715106_x_at 5.994443798
11715107_s_at 6.852757354
11715108_x_at 3.366739187
11715109_at 3.66958956
11715110_at 3.584894577
11715111_s_at 5.887865578
11715112_at 1.992804901
11715113_x_at 5.869531774
11715114_x_at 5.705243276
11715115_s_at 3.827643013
11715116_s_at 7.416754677
11715117_x_at 4.635302482
11715118_s_at 5.153112976
11715119_s_at 2.670209017

Total number of rows: 49386

Table truncated, full table size 1225 Kbytes.




Supplementary file Size Download File type/resource
GSM1587047_A1764-018.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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