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Sample GSM2322410 Query DataSets for GSM2322410
Status Public on Feb 17, 2017
Title H_PRE
Sample type RNA
 
Channel 1
Source name subcutaneous adipose tissue, female, baseline
Organism Homo sapiens
Characteristics phenotype: obese
gender: female
tissue: subcutaneous adipose tissue
treatment: hypo-caloric diet and moderate exercise
timepoint: pre-treatment
individual identifier: H
Treatment protocol Subcutaneous adipose tissue biopsies were sampled at baseline and after the 15-week intervention. In short, a small incision was made in the skin after anesthetising with lidocaine (10 mg/mL). 10-15 g tissue was extracted by use of a needle with partial vacuum after injection of 15 mL isotonic NaCl into the subcutaneous adipose tissue. Biopsies were washed in isotonic NaCl and snap-frozen in liquid nitrogen and stored at -80°C immediately.
Growth protocol 13 severely obese individuals (seven women and six men) underwent a 15-week weight loss intervention including moderate daily exercise and a hypo-caloric diet.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from approximately 350 mg of subcutaneous adipose tissue using Trizol (Invitrogen, Carlsbad, CA, USA).
Label Hy3
Label protocol 500 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.
 
Channel 2
Source name reference pool of subcutaneous adipose tissue
Organism Homo sapiens
Characteristics sample type: Common references pool (equal pool of all test samples)
Treatment protocol Subcutaneous adipose tissue biopsies were sampled at baseline and after the 15-week intervention. In short, a small incision was made in the skin after anesthetising with lidocaine (10 mg/mL). 10-15 g tissue was extracted by use of a needle with partial vacuum after injection of 15 mL isotonic NaCl into the subcutaneous adipose tissue. Biopsies were washed in isotonic NaCl and snap-frozen in liquid nitrogen and stored at -80°C immediately.
Growth protocol 13 severely obese individuals (seven women and six men) underwent a 15-week weight loss intervention including moderate daily exercise and a hypo-caloric diet.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from approximately 350 mg of subcutaneous adipose tissue using Trizol (Invitrogen, Carlsbad, CA, USA).
Label Hy5
Label protocol 500 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.
 
 
Hybridization protocol The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6th GEN (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 16.0.
Scan protocol The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).
Description H1
Hy3: 1_Exiqon_14326104_S01.txt
Hy5: 0_Exiqon_14326104_S01.txt
Data processing The quantified signals were background corrected and normalised using LOESS in marray and linear models for microarray analysis (LIMMA).
Please note that only capture probes targeting human miRNAs as well as all control probes on the array platform were included during the normalization step. Following normalization, all control probes were removed and probe set level expression data were summarized for each human miRNA by the average value of the corresponding probe sets.
 
Submission date Sep 19, 2016
Last update date Feb 19, 2017
Contact name Malene Maag Kristensen
E-mail(s) malenemk@hotmail.com
Organization name University of Copenhagen
Street address Blegdamsvej 3
City Copenhagen
ZIP/Postal code 2200
Country Denmark
 
Platform ID GPL11434
Series (1)
GSE87103 miRNAs in human subcutaneous adipose tissue: Effects of weight loss induced by hypo-caloric diet and exercise

Data table header descriptions
ID_REF
VALUE Loess normalized log2 ratio (Hy3/Hy5)

Data table
ID_REF VALUE
10138 -0.436656848
10306 0.017599141
105441 0.434745777
10899 0.44928698
10901 -0.013561038
10902 0.142710129
10903 0.363403954
10904 0.262738964
10905 0.307543659
10906 -0.352756566
10907 -0.102746455
10916 -0.473996871
10919 -0.561028627
10923 -0.620111699
10925 -0.473306222
10928 0.080779417
10936 -0.256494192
10937 0.286238732
10943 0.914616187
10946 -0.234758946

Total number of rows: 1373

Table truncated, full table size 25 Kbytes.




Supplementary file Size Download File type/resource
GSM2322410_0_Exiqon_14326104_S01.txt.gz 1.0 Mb (ftp)(http) TXT
GSM2322410_1_Exiqon_14326104_S01.txt.gz 1.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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