|
| Status |
Public on Oct 29, 2016 |
| Title |
4_BaseLine |
| Sample type |
RNA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
sibship (sampleid): 3
treatment: control
time: BaseLine
cell type: PBMC
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood mononuclear cells were isolated by density gradient centrifugation using Ficoll-paque premium (GE Healthcare, Marlborough, MA). In brief, buffy coat was isolated from 20 ml of blood and mixed with 20 times the volume of DPBS and layered over 10 ml of Ficoll-paque and centrifuged. The PBMC layer was removed, washed and centrifuged twice with DPBS. The cells were counted using a hemocytometer and processed for RNA isolation using PureLink RNA mini kit with TRIzol reagent from Ambion (Life technologies, Carlsbad, CA) per the manufacturer’s instructions. The kit includes PureLink DNase treatment to remove DNA from the sample allowing subsequent purification of RNA. The RNA concentration and quality was assessed on an Agilent BioAnalyzer 2100 RNA Nano 6000 Series II according to manufacturer’s instructions and stored at −80°C.
|
| Label |
biotin
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
Standard Illumina protocol
|
| Scan protocol |
Standard Illumina protocol
|
| Description |
4
BaseLine
|
| Data processing |
GSGX Version 1.9.0 is used to compile the raw data from the array instrument. The following Bioconductor packages are used for data processing including quality control, normalization, differential expression estimation, WGCNA.limma 3.28.17; lumi 2.24.0; genefilter 1.54.2; lumiHumanAll.db 1.22.0; data.table 1.9.6; sva 3.20.0; gplots 3.0.1; pairheatmap 1.0.1
|
| |
|
| Submission date |
Aug 30, 2016 |
| Last update date |
Oct 29, 2016 |
| Contact name |
Joel Dudley |
| E-mail(s) |
[email protected]
|
| Phone |
408-464-8258
|
| Organization name |
Mount Sinai Health System
|
| Department |
Genetics and Genomics Sciences
|
| Lab |
Dudley Laboratory & INGH
|
| Street address |
770, Lexington Ave, 15th Floor
|
| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL14951 |
| Series (1) |
| GSE86216 |
Intracoronary imaging, cholesterol efflux and transcriptomes after intensive statin treatment |
|
