|
| Status |
Public on Dec 31, 2015 |
| Title |
Subject_40_NONPREGNANT_Subcutaneous [gene-level] |
| Sample type |
RNA |
| |
|
| Source name |
non pregnant_Subcutaneous
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: Subject 40
subject status: non pregnant
tissue: adipose
region: Subcutaneous
|
| Treatment protocol |
No treatments were involved.
|
| Growth protocol |
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) .
|
| |
|
| Submission date |
Sep 25, 2015 |
| Last update date |
Dec 31, 2015 |
| Contact name |
Adi Tarca |
| E-mail(s) |
atarca@med.wayne.edu
|
| Phone |
3135775305
|
| Organization name |
Wayne State University
|
| Department |
Perinatology Research Branch (NIH/NICHD)
|
| Street address |
3990 John R
|
| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48188 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE73439 |
Changes in gene expression and splicing associated with pregnancy, labor and regions of human adipose tissue. |
|
| Relations |
| Alternative to |
GSM1893844 (exon-level analysis) |
