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Sample GSM3592091 Query DataSets for GSM3592091
Status Public on Feb 04, 2022
Title OUH_miR_138
Sample type RNA
 
Channel 1
Source name Primary breast tumour of patient without relapse
Organism Homo sapiens
Characteristics pair no.: 15
metastasis (1= yes; 0=no): 0
tumour type: IDC
esr1 expression (1=yes; 0=no): 0
lymph node status (1=positive; 0=negative): 0
status at last follow up (1=dead, 0=alive): 0
Treatment protocol After surgical removal, tumor samples were snap-frozen and stored at -80°C.
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: human breast tumour
Treatment protocol After surgical removal, tumor samples were snap-frozen and stored at -80°C.
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 without 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 Feb 05, 2019
Last update date Feb 04, 2022
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)
GSE126125 MicroRNA profiles of primary breast cancer tumors of systematically untreated and lymph node negative 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 -0.764586896
147162 0.087055691
42530 -1.475313024
42769 0.907658104
147165 1.15040824
42653 -0.241069988
145820 0.318455002
145633 0.097079253
145968 -0.757362126
42743 -0.563037147
145846 0.17557355
17752 -0.023965344
145840 0.005762732
42742 -3.056650351
42778 0.093509941
46438 -2.769093443
145746 0.487651003
9938 -0.275507688
10916 -0.334175587
145694 0.009223262

Total number of rows: 1296

Table truncated, full table size 23 Kbytes.




Supplementary file Size Download File type/resource
GSM3592091_46_1_IB.gpr.gz 721.3 Kb (ftp)(http) GPR
Processed data included within Sample table

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