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Sample GSM1164321 Query DataSets for GSM1164321
Status Public on Jul 16, 2022
Title Breast Cancer 81
Sample type RNA
 
Source name Breast tumor
Organism Homo sapiens
Characteristics filename: A1764-027
plate_pos: C3
subject_id: 81
crna_conc_ng_per_ul: 889.8
ratio_260_280: 2.32
ratio_260_230: 2.66
conc_ug_per_ul: 0.8898
final_vol_ul_1: 22
crna_yield_ug: 19.5756
crna_used_ug: 4
vol_crna_used_ul: 4.49539222297145
final_vol_ul_2: 22.5
rnase_free_water_ul: 18.0046077770285
batch: Batch1
cdna_conc_ng_per_ul: NA
cdna_yield_ug: NA
cdna_used_ug: NA
vol_cdna_used_ul: NA
dataset: FinHER
Extracted molecule total RNA
Extraction protocol RNA was extracted from FFPE tumor tissue according to the method described in Bohmann et al, Clinical Chemistry 2009
Label biotin
Label protocol Biotinylated cRNA was prepared according to Affymetrix's standard protocols
 
Hybridization protocol Hybridization was done according to Affymetrix's standard protocols for 96 array plate. The GeneTitan Hybridization, Wash and Stain kit for 3' IVT arrays was used for preparing hybridization mixes
Scan protocol 96 array plates were scanned using Affymetriix's automated GeneTitan system according to the manufacturer's instructions
Description Biotinylated cRNA was prepared according to Affymetrix's standard protocols
Data processing The probe level intensities were background adjusted using the Robust multi-array analysis (RMA) method followed by quantile normalization as impletemented in the R/Bioconductor package affy. Probe level annotations were obtained from Affymetrix’s website. In particular, we used release 32 of the NetAffx annotation files.
 
Submission date Jun 16, 2013
Last update date Jan 10, 2024
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)
GSE47994 Tumor-infiltrating lymphocytes, prognosis and trastuzumab benefit in early-stage breast cancer patients from the FinHER trial

Data table header descriptions
ID_REF
VALUE Normalized gene expression values in log2 scale.

Data table
ID_REF VALUE
11715100_at 7.36162
11715101_s_at 4.5265
11715102_x_at 6.70911
11715103_x_at 7.18683
11715104_s_at 5.43698
11715105_at 1.86164
11715106_x_at 5.25469
11715107_s_at 6.254
11715108_x_at 2.93199
11715109_at 3.37992
11715110_at 3.24052
11715111_s_at 5.39634
11715112_at 2.0176
11715113_x_at 5.68443
11715114_x_at 5.47855
11715115_s_at 3.05429
11715116_s_at 7.46176
11715117_x_at 5.41481
11715118_s_at 6.23595
11715119_s_at 3.7361

Total number of rows: 49386

Table truncated, full table size 1033 Kbytes.




Supplementary file Size Download File type/resource
GSM1164321_81.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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