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Series GSE81954 Query DataSets for GSE81954
Status Public on May 28, 2016
Title A nested case-control study to investigate drivers for metastatic disease in breast cancer (QC substudy)
Organism Homo sapiens
Experiment type Expression profiling by array
Third-party reanalysis
Summary This is a quality control (QC) substudy of GSE48091. The QC substudy comprises gene-expression profiling of re-extracted tumor RNA for a subset of the tumours in the full study. As background, a population-based cohort study of metastatic breast cancer patients was first designed. Thereafter, a case-control study nested in the corresponding population-based cohort of primary breast cancer patients was designed by selecting distant metastasis-free controls to each case. Tumor RNA was extracted in the same order. All RNA was profiled on microarrays in randomized order. For quality control, RNA was also re-extracted (new tumor piece) in a randomized order for randomly selected cases-controls sets and profiled with the rest.

Keywords: Expression profiling by array
 
Overall design The nested case-control study included 768 study subjects corresponding to 623 primary tumor samples. This QC substudy comprises 97 of the study subjects (all different primary tumor samples). Details concerning case-control status are given in the samples section.

This Series includes a re-analysis of 97 samples from GSE48091. The file "full_data_matrix.txt" includes the re-normalized values for the 97 samples from GSE48091 and the normalized values for the 97 new samples from the same patients that were analyzed together.
 
Contributor(s) Lindström LS, Lövrot J, Jauhiainen A, Czene K, Bergh J
Citation(s) 27742676
Submission date May 26, 2016
Last update date Oct 18, 2016
Contact name John Lövrot
E-mail(s) john.lovrot@ki.se
Organization name Karolinska Institutet
Department Oncology-Pathology
Street address Cancer Center Karolinska
City Stockholm
ZIP/Postal code SE-17177
Country Sweden
 
Platforms (1)
GPL10379 Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray [HuRSTA-2a520709]
Samples (97)
GSM2178377 Primary tumor breast - BCPT0736 piece 2
GSM2178378 Primary tumor breast - BCPT0151 piece 2
GSM2178379 Primary tumor breast - BCPT0169 piece 2
Relations
Reanalysis of GSM1167774
Reanalysis of GSM1167775
Reanalysis of GSM1167776
Reanalysis of GSM1167778
Reanalysis of GSM1167780
Reanalysis of GSM1167798
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Reanalysis of GSM1168394
BioProject PRJNA323489

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE81954_RAW.tar 490.4 Mb (http)(custom) TAR (of CEL)
GSE81954_full_data_matrix.txt.gz 52.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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