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Sample GSM1223795 Query DataSets for GSM1223795
Status Public on Mar 03, 2015
Title Lean 4 Visceral
Sample type RNA
 
Source name Lean 4 Visceral Adipose
Organism Homo sapiens
Characteristics tissue: Adipose
disease state: Lean
bmi: 22
age: 13
race: Mexican
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 Lean 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 7.25653 6.67007e-08
14qI-1_st 4.15556 0.00215539
14qI-1_x_st 4.63343 0.00321903
14qI-2_st 1.28854 0.404534
14qI-3_x_st 1.37273 0.145574
14qI-4_st 1.51764 0.311673
14qI-4_x_st 1.88239 0.018995
14qI-5_st 1.34148 0.618398
14qI-6_st 2.21448 3.66613e-05
14qI-6_x_st 2.64389 0.000193199
14qI-7_st 1.82472 0.0444823
14qI-8_st 2.07882 0.00803895
14qI-8_x_st 2.10133 0.0564171
14qI-9_x_st 1.63449 0.0669397
14qII-10_st 1.48242 0.656582
14qII-10_x_st 1.49536 0.584046
14qII-11_st 1.33967 0.131107
14qII-11_x_st 1.09069 0.765372
14qII-12_st 1.18018 0.973631
14qII-12_x_st 1.74465 0.0835617

Total number of rows: 25015

Table truncated, full table size 843 Kbytes.




Supplementary file Size Download File type/resource
GSM1223795_Lean_4_Visceral_miRNA-3_0_.CEL.gz 858.0 Kb (ftp)(http) CEL
GSM1223795_Lean_4_Visceral_miRNA-3_0_.rma-dabg.chp.gz 292.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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