|
| Status |
Public on Aug 16, 2013 |
| Title |
Neutrophil 1 |
| Sample type |
RNA |
| |
|
| Source name |
Neutrophil
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Neutrophils
|
| Extracted molecule |
total RNA |
| Extraction protocol |
standard Affymetrix protocol
|
| Label |
biotin
|
| Label protocol |
standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
standard Affymetrix protocol
|
| Scan protocol |
standard Affymetrix protocol
|
| Description |
Mel Greaves, Institute of Cancer Research, London
Neutrophils
|
| Data processing |
Data sets were selected for this study based on the following criteria: (1) chip platform (only data from Affymetrix Human Genome U133 Plus 2.0 expression arrays was included); (2) human primary cell; (3) cell-subset studied; (4) availability of raw data (.cel) and sample description files. Quality control (QC) of these data using the arrayQualityMetrics package in Bioconductor showed a number of chips/data sets to be of poor quality or not comparable based on the chip signal intensities. Furthermore, additional datasets were rejected from this analysis following initial analysis, as these data showed inexplicable differences in their global expression intensities when compared to data from supposedly similar cells. Out of the 1,103 chips originally selected from 105 separate studies meeting the above criteria, 745 arrays passed the criteria for further analysis on the basis of these QC arrays. All data was then subjected to RMA normalisation.
|
| |
|
| Submission date |
Aug 15, 2013 |
| Last update date |
Aug 16, 2013 |
| Contact name |
Tom C Freeman |
| E-mail(s) |
tom.freeman@roslin.ed.ac.uk
|
| Phone |
0131 651 9100
|
| Organization name |
Univeristy of Edinburgh
|
| Department |
The Roslin Institute
|
| Lab |
Systems Immunolgy
|
| Street address |
Easter Bush
|
| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH25 9RG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE49910 |
An Expression Atlas of Human Primary Cells: Inference of Gene Function from Coexpression Networks |
|
