|
| Status |
Public on Jun 01, 2016 |
| Title |
Monocytes from a premenopausal low BMD woman (KCOFS-NF19_2 PreL.CEL) |
| Sample type |
RNA |
| |
|
| Source name |
monocytes
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
bone mineral density: low BMD
state: premenopausal
cell type: monocytes
|
| Treatment protocol |
Monocyte isolation from whole blood was performed with a monocyte-negative isolation kit (Miltenyi Biotec Inc, Auburn, CA) following manufacturer's recommendation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from monocytes was extracted using Qiagen RNeasy Mini kit (Qiagen, Inc., Valencia, CA). We used Agilent Bioanalyzer (Agilent, Santa Clara, CA) to control the RNA quality before each array experiment, where RNA integrity number (RIN) should be no less than 7.0.
|
| Label |
biotin
|
| Label protocol |
Preparation of cDNA, hybridization, and scanning of the GeneChip Human Exon 1.0 ST Array was performed according to the manufacturer's protocol for the Exon 1.0 Array (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Preparation of cDNA, hybridization, and scanning of the GeneChip Human Exon 1.0 ST Array was performed according to the manufacturer's protocol for the Exon 1.0 Array (Affymetrix, Santa Clara, CA).
|
| Scan protocol |
Preparation of cDNA, hybridization, and scanning of the GeneChip Human Exon 1.0 ST Array was performed according to the manufacturer's protocol for the Exon 1.0 Array (Affymetrix, Santa Clara, CA).
|
| Data processing |
we used RMA (robust multiarray average) method to normalize the array signals through the Bioconductor’s Oligo package. After normalization of a certain dataset, we performed differential expression analysis using t test through the Bioconductor’s LIMMA (linear models for microarray data) package
|
| |
|
| Submission date |
Apr 15, 2014 |
| Last update date |
Jun 01, 2016 |
| Contact name |
Yao-Zhong Liu |
| Organization name |
Tulane University School of Public Health
|
| Department |
Dept. of Biostatistics and Bioinformatics
|
| Lab |
Center for Bioinformatics and Genomics
|
| Street address |
1440 Canal Street, Suite 2001
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE56814 |
Gene expression study of blood monocytes in pre- and postmenopausal females with low or high bone mineral density (HuEx-1_0-st-v2) |
| GSE56816 |
Gene expression study of blood monocytes in pre- and postmenopausal females with low or high bone mineral density |
|
