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Sample GSM3592089 Query DataSets for GSM3592089
Status Public on Feb 04, 2022
Title OUH_miR_136
Sample type RNA
 
Channel 1
Source name Primary breast tumour of patient without relapse
Organism Homo sapiens
Characteristics pair no.: 14
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 0.246483308
147162 -0.181430724
42530 -0.737335924
42769 0.651948426
147165 1.651473596
42653 -0.687562963
145820 0.981024461
145633 -0.218932332
145968 -0.075705307
42743 -0.119630983
145846 -0.516687064
17752 0.1965485
145840 -0.204532276
42742 -2.374613756
42778 -0.266866278
46438 -2.129156201
145746 -0.020040421
9938 0.068773382
10916 0.245467636
145694 0.085756124

Total number of rows: 1296

Table truncated, full table size 23 Kbytes.




Supplementary file Size Download File type/resource
GSM3592089_42_2_IB.gpr.gz 707.8 Kb (ftp)(http) GPR
Processed data included within Sample table

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