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High throughput sequencing of immunoglobulin (Ig) heavy (IgH) and light (IgL) chain repertoires

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE48870 | GEO | 2013/07/16

SECONDARY ACCESSION(S): PRJNA212030

REPOSITORIES: GEO

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High throughput sequencing of immunoglobulin (Ig) heavy (IgH) and light (IgL) chain repertoires

Project description: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.

2013-07-16 | E-GEOD-48870 | biostudies-arrayexpress

Comparison of gene expression profile in RAG2+ B lineage cells from the small intestinal lamina propria and RAG2+ B lineage cells from the bone marrow

Project description:We used a RAG2-GFP reporter mouse to show that RAG+ B lineage cells can be found in the small intestinal lamina proria in normally-housed mice at weaning age. We used microarry expression analysis to compare the RAG2+ population in the gut to the RAG2+ B lineage population in the bone marrow. Microarray was used to compare RAG2+ lamina propria B cells to RAG2+ bone marrow B cells. For each experiment, RAG2-GFP+ cells from 8-12 post-natal day 17-25 RAG2-GFP reporter mice were sorted from small intestinal lamina propria lymphocyte preparations and bone marrow. RNA extracted from trizol was used for the analysis. 3 independent replicates were performed.

2013-07-12 | E-GEOD-48805 | biostudies-arrayexpress

Comparison of gene expression profile in RAG2+ B lineage cells from the small intestinal lamina propria and RAG2+ B lineage cells from the bone marrow

2013-07-12 | GSE48805 | GEO

E-GEOD-48805

Project description:Comparison of gene expression profile in RAG2+ B lineage cells from the small intestinal lamina propria and RAG2+ B lineage cells from the bone marrow

2015-10-12 | E-GEOD-48805 | ExpressionAtlas

Comparison of splenic and small intestine lamina propria dendritic cells

Project description:This SuperSeries is composed of the following subset Series: GSE22127: Expression profiling of small intestine lamina propria dendritic cells GSE22128: Expression profiling of splenic dendritic cells Dendritic cells play a vital role in initiating robust immunity against pathogens as well as maintaining immunological tolerance to self antigens, food antigens and intestinal commensals. However, the intracellular signaling networks that program DCs to become tolerogenic are largely unknown. To address this, we analyzed gene expression profiles using microarray analysis of purified intestinal lamina propria DCs (CD11c+ CD11b+ DCs and CD11c+ CD11b- DCs) and compared it to splenic DCs (CD11c+ DC), from mice. We sought to determine the unique genetic profile of small intestine lamina propria CD11c+ cells compared to splenic CD11c+ cells. We performed a meta-analysis using the expression profiles of Intestinal lamina propria CD11c+ CD11b+ DCs (GSM550122), Intestinal lamina propria CD11c+ CD11b- DCs (GSM550121) and Splenic CD11c+ DCs (GSM550126). This study combined and re-normalized the microarray data from GSE22127 and GSE22128 studies. Refer to individual Series for additional details

2010-06-16 | E-GEOD-22136 | biostudies-arrayexpress

Transcriptional response of small-intestinal lamina propria CD4+ T cells to bacterial colonization

Project description:We analyzed the transcriptional profile of small-intestinal lamina propria (SI-LP) CD4+ T cells isolated from germ-free and mice monocolonized with Bifidobacterium adolescentis, SFB, and Nexabiotic (a 23-strain, Th17-inducing, probiotic mix).

2016-10-28 | GSE89261 | GEO

Expression profiling of small intestine lamina propria dendritic cells

Project description:Dendritic cells play a vital role in initiating robust immunity against pathogens as well as maintaining immunological tolerance to self antigens, food antigens and intestinal commensals. However, the intracellular signaling networks that program DCs to become tolerogenic are largely unknown. To address this, we analyzed gene expression profiles using microarray analysis of purified intestinal lamina propria DCs (CD11c+ CD11b+ DCs and CD11c+ CD11b- DCs) from mice. Keywords: Lamina propria, DCs, cell type comparison We sought to determine the expression profile of small intestine lamina propria CD11c+ cells. RNA was extracted from DCs sorted from mouse small intestine (CD11c+CD11b- and CD11c+CD11b+ cells) and hybridized on Affymetrix microarrays.

2010-06-16 | E-GEOD-22127 | biostudies-arrayexpress

The effects of Ring1A on gene expression profiles of lamina propria immune cells in DSS colitis at single cell level

Project description:immune cells in intestinal lamina propria play important roles in pathogenesis of DSS colitis. Here, we used single cell RNA sequencing (scRNA-seq) to reveale the intestinal immune landscape of DSS colitis and study the effects of Ring1A on intestinal immune cells.

2023-09-13 | GSE210866 | GEO

Microarray analysis of CD14+ CD163low cells in human intestinal lamina propria

Project description:Mouse intestinal innate immune cells have been identified as inducing Th17 cell differentiation. However, few studies have investigated innate immune cells that are involved in CD (Crohn's disiease) pathogenesis in humans. The present study aimed to identify a human intestinal lamina propria cell subset that induces Th17 cells, and to clarify its role in CD pathogenesis. Intestinal mucosa samples were obtained from patients who underwent resection of colorectal cancer or CD. Lamina propria cells (LPCs) were obtained by enzymatic digestion, and were analyzed for expression of HLA-DR, lineage markers (Lin), CD14, and CD163 using flow cytometry. Among HLA-DRhigh Lin- cells, we identified a CD14+ CD163low cell subset that was selectively present in intestinal LPCs. We identified CD14+ CD163low cells as having a potent capacity to induce Th17 cell differentiation in human intestinal lamina propria. The Th17-inducing activity of these cells was enhanced in CD patients. The Cy3-labeled cDNAs were hybridized on Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray (G4845A) in one color experiments, resulting in four individual microarrays.

2013-08-24 | E-GEOD-49066 | biostudies-arrayexpress

Single cell profiling of age-dependent and SFB induced transcriptomic changes in small intestinal epithelium and immune system

Project description:In this project, we profiled small intestinal epithelium and lamina propria immune cells from 3-, 4-, 5- and 6-weeks old wild type (WT) littermate animals using 10X droplet based RNA sequencing of single cells. In the second part, we profiled small intestinal epithelium, lamina propria immune cells as well as intraepithelial immune cells from 5-weeks old WT mice derived from Jackson laboratories and littermate colonized with SFB (segmented filamentous bacteria) 2 weeks prior to analysis, using the same approach.

2023-12-31 | E-MTAB-11982 | biostudies-arrayexpress

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