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Sample GSM1223787 Query DataSets for GSM1223787
Status Public on Mar 03, 2015
Title Obese 8 Visceral
Sample type RNA
 
Source name Obese 8 Visceral Adipose
Organism Homo sapiens
Characteristics tissue: Adipose
disease state: Obese
bmi: 33
age: 13
race: Hispanic
Sex: Female
Treatment protocol No Treatment
Growth protocol Human obese and lean visceral and subcutaneous fat were surgically acquired, dissected, and promptly cultured for 60 minutes.
Extracted molecule total RNA
Extraction protocol To isolate exosomes, we used the cell culture supernatant from the adipose tissue cultures and used ExoQuick-TC precipitation solution, according to ExoQuick-TC protocol. Total RNA was isolated following mirVana's total RNA Isolation kit.
Label biotin
Label protocol We used Affymetrix FlashTag Biotin HSR RNA Labeling Kit to label 1000 ng of cRNA from each sample.
 
Hybridization protocol For hybridization, we followed Affymetrix Gene Chip miRNA Array Procedure for Affymetrix miRNA 3.0 arrays to hybridize biotin-labeled sample.
Scan protocol We scanned the Affymetrix miRNA 3.0 arrays following the Affymetrix Command Console User Manual Instructions.
Description Obese visceral fat was promplty cultured after surgery for 60 minutes. Cell culture supernatant was used to isolate exosomes.
Data processing We analyzed the resulting data in Expression Console using RMA+DMBG (Affymetrix) and then exported it to Partek Genomics Suite for analyses. We used three-factor ANCOVA (ID*group (lean vs. obese)*adipose depot; age covariate) to compare miRNA expression, using unadjusted p ≤ 0.05 and fold change ≥ |1.2| as filters. We generated main effects for group (obesity-state) and tissue depot along with their interaction term. As a part of the overall ANCOVA, we used specific within-group (depot effects within obese or lean) and within-tissue (obesity effects within depot) contrasts. No corrections were made for multiple testing, as the primary purpose of list generation was to power pathway analysis, which mitigates false positive discovery risks.
 
Submission date Sep 04, 2013
Last update date Mar 03, 2015
Contact name Robert Freishtat
E-mail(s) rfreishtat@childrensnational.org
Organization name Children's National Medical Center
Department Center for Genetic Medicine
Street address 111 Michigan Avenue NW
City Washington
State/province DC
ZIP/Postal code 20010
Country USA
 
Platform ID GPL16384
Series (1)
GSE50574 Adipocyte-derived Exosomal miRNAs from Visceral Adipose Tissue: A Novel Mechanism for Obesity-Related Disease

Data table header descriptions
ID_REF
VALUE RMA+DMBG Signal
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
14q0_st 6.92514 6.70469e-06
14qI-1_st 4.65577 0.000659098
14qI-1_x_st 5.52072 0.00022032
14qI-2_st 1.49896 0.31169
14qI-3_x_st 1.27444 0.429716
14qI-4_st 1.18489 0.576469
14qI-4_x_st 1.95889 0.0365519
14qI-5_st 1.52246 0.526572
14qI-6_st 1.33755 0.00262028
14qI-6_x_st 1.9242 0.00254736
14qI-7_st 1.59593 0.109949
14qI-8_st 1.91534 0.00899785
14qI-8_x_st 2.58344 0.0100361
14qI-9_x_st 1.34992 0.285108
14qII-10_st 1.31589 0.828011
14qII-10_x_st 1.36216 0.621407
14qII-11_st 1.63833 0.00256386
14qII-11_x_st 1.35963 0.0356164
14qII-12_st 1.17008 0.90868
14qII-12_x_st 1.10506 0.199371

Total number of rows: 25015

Table truncated, full table size 841 Kbytes.




Supplementary file Size Download File type/resource
GSM1223787_Obese_8_Visceral.CEL.gz 913.8 Kb (ftp)(http) CEL
GSM1223787_Obese_8_Visceral.chp.gz 292.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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