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Sample GSM1909396 Query DataSets for GSM1909396
Status Public on Oct 15, 2017
Title C02 Pre
Sample type RNA
 
Source name C02 Pre Serum
Organism Homo sapiens
Characteristics biological fluid: Serum
bmi pre: 48
bmi post: 31.8
age: 41
race: AF
Sex: Female
Treatment protocol No Treatment
Growth protocol Human bariatric patient pre and post surgery serum (500 uL) was used for isolation of FABP4+ exosomes.
Extracted molecule total RNA
Extraction protocol To isolate exosomes, we used the serum from the bariatric patients (pre and post surgery) and used ExoQuick-TC precipitation solution, according to ExoQuick-TC protocol. Total RNA was isolated following mirVana's total RNA Isolation kit. We also used StemCell Technologies Magnetic Isolation Technique to isolate FABP4+ specific exosomes.
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 4.0 arrays to hybridize biotin-labeled sample.
Scan protocol We scanned the Affymetrix miRNA 4.0 arrays following the Affymetrix Command Console User Manual Instructions.
Description FABP4+ exosomes (adipocyte-derived) were isolated, amplified, and profiled from serum taken post bariatric surgery.
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 Oct 15, 2015
Last update date Oct 15, 2017
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 GPL19117
Series (1)
GSE74083 Circulating Adipose-derived Exosomal miRNAs and metabolites associated with insulin signaling are altered by gastric bypass surgery

Data table header descriptions
ID_REF
VALUE Quantification
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
MIMAT0000062_st 2.6271 0.808741
MIMAT0004481_st 2.46499 0.742192
MIMAT0010195_st 2.14735 0.769561
MIMAT0000063_st 6.54896 7.59283e-05
MIMAT0004482_st 5.87745 0.0011346
MIMAT0000064_st 4.09883 0.0891805
MIMAT0026472_st 1.84597 0.810423
MIMAT0000065_st 4.80755 0.0507379
MIMAT0004484_st 3.27171 0.128337
MIMAT0000066_st 1.87048 0.994368
MIMAT0004485_st 2.93986 0.409694
MIMAT0000067_st 2.60732 0.929136
MIMAT0004486_st 2.25635 0.914571
MIMAT0004487_st 3.08912 0.792182
MIMAT0000068_st 2.97506 0.254043
MIMAT0004488_st 3.94995 0.141163
MIMAT0000069_st 2.25635 0.319536
MIMAT0004489_st 4.0049 0.102853
MIMAT0000070_st 2.99511 0.272886
MIMAT0000071_st 1.8428 0.709492

Total number of rows: 6658

Table truncated, full table size 215 Kbytes.




Supplementary file Size Download File type/resource
GSM1909396_C02_Pre_miRNA-4_0_.CEL.gz 809.1 Kb (ftp)(http) CEL
GSM1909396_C02_Pre_miRNA-4_0_.rma-dabg.chp.gz 77.1 Kb (ftp)(http) CHP
Processed data included within Sample table

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