|
| Status |
Public on Nov 01, 2017 |
| Title |
2S189_F_CAU_N_1_12 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Stratagene UHRR reference
|
| Organism |
Homo sapiens |
| Characteristics |
control type: pool of human cell line RNA
|
| Growth protocol |
Blood (30 ml) was drawn early in the day from subjects fasted for at least eight hours to minimize the signals associated with nutritional and diurnal cycles from the microarray data. Blood was processed within fifteen minutes of the time of blood draw. Eight milliliters were collected into a tube containing EDTA and a proprietary mixture of proteinase inhibitors (Becton, Dickinson and Co., Cockeysville, MD) to provide a sample of plasma for fructosamine assays. The balance (22 ml) of blood was collected into 3 x 7 -ml Na-EDTA Vacutainer tubes (Becton, Dickinson and Co., Cockeysville, MD). Whole blood was treated with ten volumes of carbonate-buffered 150 mM NH4Cl to lyse red blood cells; the remaining leukocytes were washed and concentrated by centrifugation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA wasrecovered from leukocytes using a modified one-step acid guanidinium thiocyanate-phenol-chloroform extraction (RNA-STAT60, Tel-Test, TX). RNA was subsequently post-purified using the RNeasy Mini-kit from Qiagen in accordance with the manufacturer’s instructions. RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer 2100. RNA isolation from samples was completed within two hours, exceeding the standards of the Consortium for Expression Profiles in Sepsis.
|
| Label |
Cy-3
|
| Label protocol |
500 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.
|
| |
|
| Channel 2 |
| Source name |
Whole blood, mononuclear cell extract
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: mononuclear
gender: F
ancestry: CAU
obstructive_cad: N
cad class: 1
cxcl5 rank: 12
bmi: 23.0008
diabetes: N
hyperlipid: Y
hypertension: Y
scan_date_id: 26-May
batchid: E
|
| Growth protocol |
Blood (30 ml) was drawn early in the day from subjects fasted for at least eight hours to minimize the signals associated with nutritional and diurnal cycles from the microarray data. Blood was processed within fifteen minutes of the time of blood draw. Eight milliliters were collected into a tube containing EDTA and a proprietary mixture of proteinase inhibitors (Becton, Dickinson and Co., Cockeysville, MD) to provide a sample of plasma for fructosamine assays. The balance (22 ml) of blood was collected into 3 x 7 -ml Na-EDTA Vacutainer tubes (Becton, Dickinson and Co., Cockeysville, MD). Whole blood was treated with ten volumes of carbonate-buffered 150 mM NH4Cl to lyse red blood cells; the remaining leukocytes were washed and concentrated by centrifugation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA wasrecovered from leukocytes using a modified one-step acid guanidinium thiocyanate-phenol-chloroform extraction (RNA-STAT60, Tel-Test, TX). RNA was subsequently post-purified using the RNeasy Mini-kit from Qiagen in accordance with the manufacturer’s instructions. RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer 2100. RNA isolation from samples was completed within two hours, exceeding the standards of the Consortium for Expression Profiles in Sepsis.
|
| Label |
Cy-5
|
| Label protocol |
500 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.
|
| |
|
| |
| Hybridization protocol |
Labeled subject cRNA was co-hybridized to Agilent G4112F Whole Human Genome 4x44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.
|
| Scan protocol |
Scanned on an Axon Instruments GenePix 4000b scanner.
|
| Data processing |
The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (v9.5.1.1 Agilent).The log expression ratios produced during the normalization step are provided.
|
| |
|
| Submission date |
Nov 18, 2016 |
| Last update date |
Nov 01, 2017 |
| Contact name |
Jonathan C Schisler |
| E-mail(s) |
schisler@unc.edu
|
| Phone |
919-843-8708
|
| Organization name |
The University of North Carolina at Chapel Hill
|
| Department |
McAllister Heart Institute
|
| Lab |
Schisler Lab
|
| Street address |
MBRB, Rm 2340C
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7126 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE90074 |
Gene expression data from Phase 2 of the SAMARA study (Supporting a Multi-disciplinary Approach to Researching Atherosclerosis) |
| GSE90076 |
Clinical Evidence Supports a Protective Role for CXCL5 in Coronary Artery Disease Progression in the Elderly |
|
