E-GEOD-48870 - Transcription profiling by high throughput sequencing of mice colonized for 7 days vs germ free mice

Released on 16 July 2013, last updated on 11 May 2016
Mus musculus
Samples (40)
Protocols (3)
We used 454 sequencing to assess the repertoire of B cell subsets from bone marrow, spleen, and small intestinal lamina propria from two mouse strains. We used a RAG2-GFP reporter mouse strain (129Sve background) to isolate CD19+ RAG2+ B lineage cells from bone marrow and small intestinal lamina propria and total splenic B cells. We used 5' RACE to amplify cDNA libraries using primers specific for the mu constant region of IgH and the Ig kappa constant region. We also used this technique to analyze total B cell libraries from Swiss Webster germ-free mice to compare to littermate controls that were cohoused with regular specific pathogen free (SPF) mice for 7 days. Examination of the Ig kappa repertoire and IgH repertoire in RAG2+ bone marrow B lineage cells compared to RAG2+ small intestinal lamina propria B lineage cells or total splenic B cells. There are 8 (Ig kappa) or 4 (IgH) independent experiments comparing repertoires in RAG2-GFP mice. Each experiment in RAG2-GFP+ mice consisted of a pool of 8-12 mice. There are 3 experiments comparing germ-free to colonized mouse total B cell repertoires, each consisting of one mouse per condition.
Experiment type
RNA-seq of coding RNA 
Frederick Alt <geo@ncbi.nlm.nih.gov>, Andrew P Portuguese, Duane R Wesemann, Frederick W Alt, Jennifer M.Magee, Kendra Cluff-Jones, Michael P Gallagher, Robin M Meyers, Rohit A Panchakshari, Scott J Rodig, Thomas B Kepler
Microbial colonization influences early B-lineage development in the gut lamina propria. Wesemann DR1, Portuguese AJ, Meyers RM, Gallagher MP, Cluff-Jones K, Magee JM, Panchakshari RA, Rodig SJ, Kepler TB, Alt FW. , Europe PMC 23965619
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-48870.idf.txt
Sample and data relationshipE-GEOD-48870.sdrf.txt
Additional data (1)E-GEOD-48870.additional.1.zip