|
| Status |
Public on Mar 12, 2012 |
| Title |
infant_rsv_546 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood mononuclear cells(PBMCs)
|
| Organism |
Homo sapiens |
| Characteristics |
age (months): 9.73
Sex: M
cell type: peripheral blood mononuclear cells
infection: rsv
|
| Treatment protocol |
Blood samples were obtained from patients with acute RSV or Influenza infection or Healthy Controls
|
| Growth protocol |
Blood samples (3-6 ml) were collected in acid-citrate-dextrose tubes (BD Vacutainer) and delivered at room temperature for microarray processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs were isolated within 6 h of sample collection by density gradient centrifugation using ficoll-hypaque and lysed in RLT reagent (Qiagen) with β-mercaptoethanol. Samples were run blind and in batches by the same laboratory team to ensure standardization of quality and handling. From 2-5 ug of total RNA, cDNA was generated as a template for single-round in vitro transcription with biotin-labeled nucleotides using the Affymetrix cDNA Synthesis and In Vitro Transcription kits (Affymetrix Inc.).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA targets were purified and hybridized to the Affymetrix HG-U133 plus 2.0 Chip arrays according to the manufacturer’s standard protocols
|
| |
|
| Hybridization protocol |
Biotinylated cDNA targets were then purified and hybridized to the Affymetrix HG-U133 plus 2.0 Chip arrays according to the manufacturer’s standard protocols
|
| Scan protocol |
Arrays were scanned using a laser confocal scanner (Agilent).
|
| Description |
gene expression profile in infants with rsv infection
|
| Data processing |
Raw signal intensity signal intensity values were normalized to the mean intensity of all measurements per gene chip and scaled to a target intensity value of 500 using the MAS 5.0 global scaling method to adjust for possible chip-to-chip variations in hybridization intensities (GeneChip Operating System version 1.0).The values were then normalized with Genespring GX 7.3.1.The values of RSV samples were normalized to the median of their respective healthy controls (controls for rsv) and the values for Influenza samples were nomalized to the median of their respective healthy controls( controls for Influenza).
|
| |
|
| Submission date |
Dec 06, 2011 |
| Last update date |
Nov 30, 2020 |
| Contact name |
Damien Chaussabel |
| E-mail(s) |
DChaussabel@benaroyaresearch.org
|
| Organization name |
Baylor Institute for Immunology Research
|
| Street address |
3434 Live Oak
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75204 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE32140 |
The response of PBMCs and primary airway epithelial cells to Influenza and RSV virus |
| GSE34205 |
Transcriptional profile of PBMCs in patients with acute RSV or Influenza infection |
|
| Relations |
| Reanalyzed by |
GSE122511 |
| Reanalyzed by |
GSE162329 |
