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Sample GSM2756364 Query DataSets for GSM2756364
Status Public on Feb 16, 2018
Title OUH_miR_087
Sample type RNA
 
Channel 1
Source name Primary breast tumour of patient with relapse
Organism Homo sapiens
Characteristics tissue: primary breast tumour
gender: female
pair no.: 44
metastasis (1= yes; 0=no): 1
tumour type: Papillary carcinoma
esr1 expression (1=yes; 0=no): 1
lymph node status (1=positive; 0=negative): 0
status at last follow up (1=dead, 0=alive): 1
Treatment protocol After surgical removal, tumor samples were snap-frozen and stored at -80°C.
Growth protocol not applicable
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tumor samples with Trizol (Invitrogen) and further purified with the RNeasy micro kit (Qiagen), including DNase treatment. NanoDrop Spectrophotometer (NanoDrop Technologies) was used for RNA quantification. The quality of extracted RNA was assessed with Bioanalyzer 2100 (Agilent Technologies) using the RNA 6000 Nano Kit (Agilent Technologies).
Label Hy3
Label protocol The miRCURY Power labeling kit (Exiqon), miRCURY LNA Array hybridization buffer (Exiqon) and miRCURY LNA Array Washing buffer kit (Exiqon) were used for sample labelling, hybridization and washing, respectively.
 
Channel 2
Source name common reference pool of all samples
Organism Homo sapiens
Characteristics tissue: primary breast tumour
gender: female
Treatment protocol After surgical removal, tumor samples were snap-frozen and stored at -80°C.
Growth protocol not applicable
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tumor samples with Trizol (Invitrogen) and further purified with the RNeasy micro kit (Qiagen), including DNase treatment. NanoDrop Spectrophotometer (NanoDrop Technologies) was used for RNA quantification. The quality of extracted RNA was assessed with Bioanalyzer 2100 (Agilent Technologies) using the RNA 6000 Nano Kit (Agilent Technologies).
Label Hy5
Label protocol The miRCURY Power labeling kit (Exiqon), miRCURY LNA Array hybridization buffer (Exiqon) and miRCURY LNA Array Washing buffer kit (Exiqon) were used for sample labelling, hybridization and washing, respectively.
 
 
Hybridization protocol Hybridization, washing, and scanning (Agilent G2565CA Microarray scanner) were performed according to the recommendations provided by Exiqon.
Scan protocol Scanned images were imported into GenePixPro6.0 software (Molecular Devices) for quality control and raw data extraction.
Description Total RNA extracted from fresh frozen primary breast tumour of a female patient with relapse
Data processing Signals from 3 spots were compiled, only human microRNAs were selected, the R-package limma was used for LOESS normalization and quantile normalization of raw signal intensities, and the ComBat function embedded in the sva R-package was used for adjustment of the normalized intensities and to eliminate potential batch effects
 
Submission date Aug 28, 2017
Last update date Jan 29, 2019
Contact name Ines Block
Organization name Odense University Hospital
Department Department of Clinical Genetics
Street address J.B. Winsløws Vej 4
City Odense
ZIP/Postal code 5000
Country Denmark
 
Platform ID GPL23960
Series (1)
GSE103161 MicroRNA profiles of 110 primary breast cancer tumors of systemically untreated, lymph node negative and estrogen receptor positive patients

Data table header descriptions
ID_REF
VALUE normalized log2 ratio between Hy3 (individual samples) and Hy5 (common references);

Data table
ID_REF VALUE
17888 0.083314526
147162 -0.178244475
42530 -1.142162151
42769 0.25044173
147165 0.660759392
42653 -0.485744069
145820 0.278826795
145633 -0.215730695
145968 -0.608194481
42743 -0.302846401
145846 -1.026450868
17752 0.061651739
145840 -0.186420169
42742 -2.653065015
42778 -0.042931897
46438 -2.073845273
145746 -0.640756952
9938 -0.151868096
10916 0.035548848
145694 -0.183308057

Total number of rows: 1296

Table truncated, full table size 23 Kbytes.




Supplementary file Size Download File type/resource
GSM2756364_OUH_miR_087.gpr.gz 709.4 Kb (ftp)(http) GPR
Processed data included within Sample table

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