|
| Status |
Public on Nov 15, 2013 |
| Title |
PBMCs from sham-operated rat, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: peripheral blood mononuclear cells
samples collection: 2 months after sham-surgery
size of myocardial infarction: lack of an infarct area
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from left ventricular (LV) tissue and peripheral blood mononuclear cells (PBMCs) samples was isolated using MagNA Pure Compact System (Roche Diagnostics GmbH, Germany) according to the manufacturer's recommendations. LVs were previously homogenized by MagNA Lyser Instrument. The amount of RNA was quantified by UV absorption (Nanodrop, LabTech International, UK) and its quality was determined using an Agilent 2100 Bioanalizer© and RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA). For all RNA samples the RNA integrity number value was above eight.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled ssDNA were prepared from 100 ng total RNA by using the Ambion® WT Expression Kit followed by Affymetrix® GeneChip® WT Terminal Labeling Kit according to the manufacturer's instruction.
|
| |
|
| Hybridization protocol |
Following fragmentation, 5.5 ug ssDNA were hybridized for 16 hr at 45˚C on GeneChip® Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using an Affymetrix GCS 3000 GeneArray Scanner.
|
| Description |
Gene expression data from peripheral blood mononuclear cells (PBMCs) of sham-operated rat
|
| Data processing |
The data were analyzed with the Partek Genomics Suite software (Partek Inc, St. Louis, MO, USA) using RMA (robust multiarray average) background correction, quantile normalization, median polish method for probesets summarization, and log values of probes signals using base 2.
|
| |
|
| Submission date |
May 29, 2013 |
| Last update date |
Nov 15, 2013 |
| Contact name |
Dorota Anna Tulacz |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Biochemistry and Biophysics of the Polish Academy of Sciences
|
| Department |
Department of Genetics
|
| Street address |
Pawinskiego 5a
|
| City |
Warszawa |
| ZIP/Postal code |
02-106 |
| Country |
Poland |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE47495 |
Transcriptional profiling of left ventricle and peripheral blood cells in rats with post-myocardial infarction |
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