|
| Status |
Public on Dec 09, 2014 |
| Title |
P71111019918_9 |
| Sample type |
RNA |
| |
|
| Source name |
Whole blood sample, HV
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: healthy
tissue: whole blood
gender: female
|
| Treatment protocol |
Blood was collected in a PAXgene® tube, incubated at room temperature for 4h for RNA stabilization and then stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from whole blood using the PAXgeneTM Blood RNA System Kit (PreAnalytix, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
Cy3
|
| Label protocol |
The cRNA labeling was performed according to Protocol from Agilent Technologies Inc. (Santa Clara, CA) using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) following the two-colour manufacturer's protocol. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
cRNA samples were hybridized to an Agilent Technologies Human Gene Expression 8x60K Microarray during 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies). The hybridization slides were washed, stabilized, dried, and immediately scanned.
|
| Scan protocol |
Scanned with an Agilent Technologies Microarray Scanner using default parameters (protocol GE2_107_Sep09 and Grid: 028004_D_F_20110325). Each sample represents one channel of a dual-channel array.
|
| Description |
P71111019918_9_13295_1_3
This Sample represents one channel of a dual-channel array.
|
| Data processing |
Data extraction of median feature intensity without background subtraction was peformed with Feature Extraction software v10.7.1.1 (gMedianSignal or rMedianSignal column) (Agilent Technologies). In order to remove systemic signal intensity bias between each array, median feature intensity were normalized with the function lowess (Locally weighted scatterplot smoothing) method, and then spots with half of the samples exhibiting signal less than the mean of all median signals were removed (threshold: 90.83). 30,146 spots were kept out of 58,717.
|
| |
|
| Submission date |
May 25, 2012 |
| Last update date |
Dec 09, 2014 |
| Contact name |
Richard Danger |
| E-mail(s) |
richard.danger@univ-nantes.fr
|
| Phone |
+33 2 40 08 75 65
|
| Organization name |
CHU Nantes - INSERM- Nantes Universite
|
| Department |
U1064
|
| Lab |
CR2TI
|
| Street address |
30 Boulevard Jean Monnet
|
| City |
Nantes |
| ZIP/Postal code |
44035 |
| Country |
France |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE38267 |
Gene expression profiling in blood of patients with chronic respiratory failure |
|
