|
| Status |
Public on Jan 29, 2011 |
| Title |
Spleen Follicular B cells from B6 mouse #92769 |
| Sample type |
RNA |
| |
|
| Source name |
B6 Spleen Follicular B cells
|
| Organism |
Mus musculus |
| Characteristics |
animal id: B6 mouse #92769
cell type: Spleen Follicular B cells
genetic background: B6
genotype: wild type
|
| Treatment protocol |
Cells were obtained from control B6 mice or mice transgenic for KLF3 (CD19:KLF3)
|
| Growth protocol |
Viable spleen follicular B cells and MZB cells were sorted based on C19, CD21 and CD23 expression (sytox_blue_neg, CD19_pos, CD21_int, CD23_pos and sytox_blue_neg, CD19_pos, CD21_high, CD23_neg respectively)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using the Experion automated electrophoresis system (Bio-Rad).
|
| Label |
biotin
|
| Label protocol |
Total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit, which is based on the Eberwine amplification protocol.
|
| |
|
| Hybridization protocol |
The biotinylated cRNA was hybridized onto Illumina MouseRef-8 BeadChips V2 at 58oC for 20 hrs
|
| Scan protocol |
Fluoresent array images were collected using Illumina BeadStation 500GX scanner and image intensity data were extracted using Illumina BeadStudio v3.
|
| Description |
Spleen Follicular B cells from B6 mouse #92769
|
| Data processing |
Illumina probe data were exported from BeadStudio as raw data and were screened for quality. Samples failing chip visual inspection and control examination were removed. The R software was used to quantile-normalized the probe intensities, and to minimun replace (surrogate-replacement policy) values below backround using the mean backround value of the built-in Illumina probe controls as an alternative to background substraction (which may introduce negative values) to reduce ‘over inflated’ expression ratios in subsequent steps.
|
| |
|
| Submission date |
Jan 28, 2011 |
| Last update date |
Jan 29, 2011 |
| Contact name |
Jean-Philippe Goulet |
| E-mail(s) |
jp.goulet@umontreal.ca
|
| Organization name |
Université de Montréal
|
| Street address |
C.P. 6128, succursale Centre-ville
|
| City |
Montréal |
| State/province |
Québec |
| ZIP/Postal code |
H3X 3J7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE26948 |
Programming of marginal zone B cell fate by basic krüppel-like factor (BKLF/KLF3) |
|
