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Sample GSM1223781 Query DataSets for GSM1223781
Status Public on Mar 03, 2015
Title Obese 3 Visceral
Sample type RNA
 
Source name Obese 3 Visceral Adipose
Organism Homo sapiens
Characteristics tissue: Adipose
disease state: Obese
bmi: 50
age: 17.5
race: AF
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 7.34184 4.5772e-08
14qI-1_st 4.27038 0.000230215
14qI-1_x_st 4.70626 0.000648127
14qI-2_st 1.24333 0.464391
14qI-3_x_st 1.25921 0.223524
14qI-4_st 1.47543 0.104305
14qI-4_x_st 1.79762 0.00740225
14qI-5_st 1.92025 0.174991
14qI-6_st 1.76793 0.000309238
14qI-6_x_st 2.54902 0.00010956
14qI-7_st 1.62113 0.0417144
14qI-8_st 1.7633 0.0159553
14qI-8_x_st 2.09669 0.0344057
14qI-9_x_st 1.36467 0.289737
14qII-10_st 1.42577 0.763121
14qII-10_x_st 1.35689 0.610853
14qII-11_st 1.26813 0.0434083
14qII-11_x_st 1.28947 0.112906
14qII-12_st 1.1393 0.910776
14qII-12_x_st 1.1638 0.234862

Total number of rows: 25015

Table truncated, full table size 845 Kbytes.




Supplementary file Size Download File type/resource
GSM1223781_Obese_3_Visceral_miRNA-3_0_.CEL.gz 855.1 Kb (ftp)(http) CEL
GSM1223781_Obese_3_Visceral_miRNA-3_0_.chp.gz 292.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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