Paired visceral and subcutaneous adipose tissue samples were obtained after an eight-hour fast. Subcutaneous adipose tissue samples were collected at the site of a transverse lower abdominal incision, in the middle of the Pfannenstiel incision, from the deeper strata of subcutaneous fat. Visceral samples were obtained from the most distal portion of the greater omentum.(Visceral and subcutaneous adipose tissues were collected using Metzenbaum scissors and measured approximately 1.0 cm3. Tissues were snap-frozen in liquid nitrogen, and were kept at –80°C until use.
Extracted molecule
total RNA
Extraction protocol
Total RNA was isolated from snap-frozen adipose tissue samples using TRI Reagent® (Ambion®, Life Technologies Corporation, Austin, TX, USA) combined with the Qiagen RNeasy Lipid Tissue Kit protocol (Qiagen, Valencia, CA, USA), according to the manufacturers’ recommendations. The RNA concentrations and the A260 nm/A280 nm ratios were assessed using a NanoDrop® 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA integrity numbers were determined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Wilmington, DE, USA).
Label
biotin
Label protocol
Standard Affymetrix Exon Array labeling protocol.
Hybridization protocol
Standard Affymetrix Exon Array hyb protocol.
Scan protocol
Standard Affymetrix Exon Array scan protocol.
Data processing
Probe intensities were summarized and processed with RMA implemented in arroma.affymetrix package in R-3.2.2. For transcript level summaries ExonRmaPlm function from arroma.affymetrix was used (option mergeGroups=TRUE), while for probeset (exon) level summaries the option mergeGroups=FALSE was used. probe group file: HuEx-1_0-st-v2.na30.hg19.probeset.csv meta-probeset file: HuEx-1_0-st-v2.na30.hg19.transcript.csv Log2 transformed probeset (exon) and transcript (group) level expression summaries for core transcripts based on NetAffx Nov. 12, 2007 (R3) (HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf) .
