|
| Status |
Public on Feb 12, 2017 |
| Title |
Subject B_subcutaneous_1000 nM dexamethasone |
| Sample type |
RNA |
| |
|
| Source name |
subcutaneous_1000 nM dexamethasone
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: pooled, two subjects with BMI 41 (AA, F, 54 yrs) and 42.5 (H, F, 28 yrs)
treatment: dexamethasone
depot: subcutaneous
concentration: 1000 nM
tissue: adipose tissue explant
|
| Treatment protocol |
Media (with same additions/treatments) was exchanged every other day and on the day prior to processing on d7.
|
| Growth protocol |
organ culture protocol: 300-400 mg of minced adipose tissue fragments (5-10 mg) were placed in organ culture in 15 ml of Medium 199 with the treatments as previously described (Lee et al, Am J Physiol Endocrinol Metab. 2011 Mar;300(3):E571-80)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Trizol reagent (Life Technologies, Carlsbad, CA), cleaned with RNeasy MiniElute Cleanup Kit (Qiagen, Germantown, MD).
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
B-S4
Gene expression data from subcutaneous adipose tissue explant treated with 1000 nM dexamethasone.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1) and an Entrez Gene-specific probeset mapping (version 14.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan. NOTE: RMA normalization was performed using additional samples, and so the gene expression values in this GEO record cannot be reproduced exactly from these samples alone.
|
| |
|
| Submission date |
Oct 20, 2016 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL15034 |
| Series (1) |
| GSE88966 |
Depot dependent effects of dexamethasone on gene expression in human omental and abdominal subcutaneous adipose tissues from obese women. |
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