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Sample GSM1909404 Query DataSets for GSM1909404
Status Public on Oct 15, 2017
Title C08 Pre
Sample type RNA
Source name C08 Pre Serum
Organism Homo sapiens
Characteristics biological fluid: Serum
bmi pre: 51.3
bmi post: 39
age: 39
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
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
VALUE Quantification

Data table
MIMAT0000062_st 2.63967 0.552547
MIMAT0004481_st 2.01135 0.738736
MIMAT0010195_st 2.16172 0.543231
MIMAT0000063_st 8.2532 5.13649e-07
MIMAT0004482_st 7.60167 1.36549e-06
MIMAT0000064_st 3.1661 0.0841303
MIMAT0026472_st 2.74207 0.621635
MIMAT0000065_st 3.90916 0.0327632
MIMAT0004484_st 3.23106 0.351163
MIMAT0000066_st 2.31083 0.898219
MIMAT0004485_st 1.93299 0.899204
MIMAT0000067_st 1.88387 0.9424
MIMAT0004486_st 1.81731 0.929095
MIMAT0004487_st 2.45819 0.768443
MIMAT0000068_st 2.08506 0.516739
MIMAT0004488_st 2.99384 0.33301
MIMAT0000069_st 1.92039 0.962822
MIMAT0004489_st 4.27085 0.043705
MIMAT0000070_st 2.50517 0.542693
MIMAT0000071_st 1.58638 0.851851

Total number of rows: 6658

Table truncated, full table size 216 Kbytes.

Supplementary file Size Download File type/resource
GSM1909404_C08_Pre_miRNA-4_0_.CEL.gz 898.7 Kb (ftp)(http) CEL
GSM1909404_C08_Pre_miRNA-4_0_.rma-dabg.chp.gz 77.6 Kb (ftp)(http) CHP
Processed data included within Sample table

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