Comparative gene expression profiles of T-dependent and T-independent germinal centre B cells in mice

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PubMed ID: none
Contact: Diego G Silva

Image:email_GSE8906.png
John Curtin School of Medical Research

Species: Mus musculus
Platform: Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A
Number of Samples: 8
Date Range: 12/31/1969 - 12/31/1969
Experiment Quality: 97.75
4.34 %
Link to Repository: GSE8906
Original Intensity Data: Download
Clean Intensity Data: Download
Original PLIER Data: Download
Clean PLIER Data: Download
Clean CEL Files:
Data Rank:

Selection of B cells subjected to hypermutation in germinal centres (GC) during T-dependent (TD) antibody responses yields memory cells and long-lived plasma cells that produce high affinity antibodies biased to foreign antigens rather than self-antigens. GC also form in T-independent (TI) responses to polysaccharide antigens but failed selection results in GC involution and memory cells are not generated. To date there are no markers that allow phenotypic distinction of T-dependent and T-independent germinal centre B cells. We have now compared the global gene expression of GC B cells purified from mice immunized with either TD or TI antigens and identified eighty genes that are differentially expressed in TD GC.

Design: QMxB6 F1 mice were immunised with T-independent antigens (NP-Ficoll) or T-dependent antigens (NP-CGG). T-dependent responses were analysed in carrier primed mice and non-carrier primed mice. The kinetics in carrier primed mice are comparable to those of TI-2 antigens, and thus, both of these groups were analysed 4 days after immunization with soluble antigen. The response in non-carrier primed mice peaks later, and was therefore analysed on day 10 after immunization. Germinal centre B cells were MACS enriched and then FACS sorted according to GL-7 and B220 expression. Sorted B cells from the relevant mice were pooled (4-10 mice per sample). Each sample thus contains B cells from different mice, and the replicates are biological, not technical replicates.

Type: T-dependent and T-independent germinal center B cells


Contents

[edit] Contributors

  • Carola G Vinuesa
  • Di Yu
  • Diego G Silva
  • Chris G Goodnow
  • Mike P Cooke

[edit] Protocols

[edit] References

[edit] Links

GEO Accession for this experiment: GSE8906. (Public on Sep 05 2007)

RAW data: tar file.

[edit] Analysis

Gel Plots

Before Normalization

After Normalization & Cleaning

[edit] Samples/Quality Control

Sample Date Scanned Source Link Probe Variance Data Artifact Mask Quality Score
Resting B cells (pooled from 6 mice) 1 GSM225630 Probe variance for Resting B cells (pooled from 6 mice) 1 Artifact mask for Resting B cells (pooled from 6 mice) 1 97.8478
4.09 %
Resting B cells (pooled from 9 mice) 2 GSM225631 Probe variance for Resting B cells (pooled from 9 mice) 2 Artifact mask for Resting B cells (pooled from 9 mice) 2 96.6377
7.45 %
Day 4 T-dependent GC B cells in carrier primed mice (pooled from 6 mice) 1 GSM225632 Probe variance for Day 4 T-dependent GC B cells in carrier primed mice (pooled from 6 mice) 1 Artifact mask for Day 4 T-dependent GC B cells in carrier primed mice (pooled from 6 mice) 1 97.7768
3.51 %
Day 4 T-dependent GC B cells in carrier primed mice (pooled from 9 mice) 2 GSM225633 Probe variance for Day 4 T-dependent GC B cells in carrier primed mice (pooled from 9 mice) 2 Artifact mask for Day 4 T-dependent GC B cells in carrier primed mice (pooled from 9 mice) 2 98.7272
0.71 %
Day 10 T-dependent GC B cells in non-carrier-primed mice (pooled from 6 mice) 1 GSM225634 Probe variance for Day 10 T-dependent GC B cells in non-carrier-primed mice (pooled from 6 mice) 1 Artifact mask for Day 10 T-dependent GC B cells in non-carrier-primed mice (pooled from 6 mice) 1 98.3792
1.33 %
Day 10 T-dependent GC B cells in non-carrier-primed mice (pooled from 6 mice) 2 GSM225635 Probe variance for Day 10 T-dependent GC B cells in non-carrier-primed mice (pooled from 6 mice) 2 Artifact mask for Day 10 T-dependent GC B cells in non-carrier-primed mice (pooled from 6 mice) 2 98.3672
2.04 %
Day 4 T-independent GC B cells (pooled from 4 mice) 1 GSM225636 Probe variance for Day 4 T-independent GC B cells (pooled from 4 mice) 1 Artifact mask for Day 4 T-independent GC B cells (pooled from 4 mice) 1 96.2016
11.63 %
Day 4 T-independent GC B cells (pooled from 10 mice) 2 GSM225637 Probe variance for Day 4 T-independent GC B cells (pooled from 10 mice) 2 Artifact mask for Day 4 T-independent GC B cells (pooled from 10 mice) 2 98.0404
3.95 %
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