|
| Status |
Public on Oct 27, 2016 |
| Title |
M3_150 |
| Sample type |
RNA |
| |
|
| Source name |
total RNA (globin reduced)
|
| Organism |
Macaca fascicularis |
| Characteristics |
tissue: Whole Blood
ChIP: 6
hyb chamber: 2
dataset: Training
synchroset: No
pittid: 21510
monkeyid: M3
time point: 150
infection time: M5
clinical status: Latent
FDG avidity: 0
FDG group: Low
hemoglobin: 12.9
hematocrit: 37.9
wbc: 13.6
platelet: 392
per neutrophils: 69
per lymphocytes: 27
per monocytes: 3
per eosinophils: 1
per basophils: 0
abs neutrophils: 9384
abs lymphocytes: 3672
abs monocytes: 408
abs eosinophils: 0
per monos by lymphos: 0.11111111
abs monos by lymphos: 0.11111111
per lymphosstained: 59.5
per cd3stained: 83.9
per lymphosstained: 57.5
per cd8: 32
per cd16pos cd3neg: 8.19
per cd20: 7.11
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from Applied Biosystems Tempus Blood RNA Tubes using the Ambion MagMax-96 total RNA Isolation kits, Globin message reduction was conducted using Ambion GlobinClear Human 96 Kits
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared using Illumina Totalprep-96 Amplification Kits with 250ng input
|
| |
|
| Hybridization protocol |
Standard Illumina HT-12 V4 hybridization protocol
|
| Scan protocol |
Standard Illumina iScan protocol
|
| Description |
M3_150
6303281024_E.AVG_Signal
|
| Data processing |
Following background subtraction, the raw signal intensities extracted with Illumina Genome Studio v2010.1 Gene Expression 1.6.0 software were scaled to the mean intensity of the datase to yield the Matrix normalized data available here. Data was further filtered on probes for which pval detection was below 0.01 in at least one sample were kept for analysis. The ComBat method (Johnson et al, Biostatistics, 2007) was used on those normalized data to correct for batch effects (namely a small Hybridization chamber effect and the Training/test set effect), that was identified through Principal Variance Component Analysis (PVCA)
|
| |
|
| Submission date |
Jul 07, 2016 |
| Last update date |
Oct 27, 2016 |
| Contact name |
Jason A Skinner |
| E-mail(s) |
[email protected]
|
| 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 |
GPL10558 |
| Series (1) |
| GSE84152 |
Early whole blood transcriptional signatures are associated with severity of lung inflammation in cynomolgus macaques with Mycobacterium tuberculosis infection |
|
