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Status |
Public on Jan 29, 2011 |
Title |
Spleen Follicular B cells from CD19:KLF3 mouse #92759 |
Sample type |
RNA |
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Source name |
CD19:KLF3 Spleen Follicular B cells
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Organism |
Mus musculus |
Characteristics |
animal id: CD19:KLF3 mouse #92759 cell type: Spleen Follicular B cells genetic background: B6 genotype: CD19:KLF3 transgenic
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Treatment protocol |
Cells were obtained from control B6 mice or mice transgenic for KLF3 (CD19:KLF3)
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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)
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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).
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Label |
biotin
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Label protocol |
Total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit, which is based on the Eberwine amplification protocol.
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Hybridization protocol |
The biotinylated cRNA was hybridized onto Illumina MouseRef-8 BeadChips V2 at 58oC for 20 hrs
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Scan protocol |
Fluoresent array images were collected using Illumina BeadStation 500GX scanner and image intensity data were extracted using Illumina BeadStudio v3.
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Description |
Spleen Follicular B cells from CD19:KLF3 mouse #92759
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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.
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Submission date |
Jan 28, 2011 |
Last update date |
Jan 29, 2011 |
Contact name |
Jean-Philippe Goulet |
E-mail(s) |
jp.goulet@umontreal.ca
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Organization name |
Université de Montréal
|
Street address |
C.P. 6128, succursale Centre-ville
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City |
Montréal |
State/province |
Québec |
ZIP/Postal code |
H3X 3J7 |
Country |
Canada |
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|
Platform ID |
GPL6885 |
Series (1) |
GSE26948 |
Programming of marginal zone B cell fate by basic krüppel-like factor (BKLF/KLF3) |
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