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Targeted chromatin profiling reveals novel enhancers in Ig heavy and light chain loci.

ABSTRACT: Chip-chip from pro-B cells from Rag1KO mice for H3K27ac and RNA Pol II Identification of novel enhancers from Ig heavy and light chain loci

ORGANISM(S): Mus musculus

PROVIDER: GSE53766 | GEO | 2014/01/03

SECONDARY ACCESSION(S): PRJNA232844

REPOSITORIES: GEO

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Targeted chromatin profiling reveals novel enhancers in Ig heavy and light chain loci.

Project description:Chip-chip from pro-B cells from Rag1KO mice for H3K27ac and RNA Pol II Identification of novel enhancers from Ig heavy and light chain loci Rag1KO pro-B epigenetic landscape at Ig heavy and light chain loci

2014-01-03 | E-GEOD-53766 | biostudies-arrayexpress

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

Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci.

Project description: Not available

| S-EPMC4096788 | biostudies-literature

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

2013-07-16 | GSE48870 | GEO

Intrinsic toxicity of LCDD monoclonal Ig free light chain on plasma cells (PC)

Project description:We analyzed the transcriptome (RNA-seq) of mouse plasma cells (PC) expressing a human Ig light chain from a patient suffering light chain deposition disease (LCDD) as compared to control plasma cells (WT and DH-LMP2A, the latter producing no complete immunoglobulins, only free Ig light chains). Ig light chains causing LCDD present structural peculiarities leading to their aggregation and deposition into tissues and organs, mainly the kidney. We sought to determine if plasma cells producing these abnormal Ig could present specific phenotypes. The aim of the present study is to analyse the transcriptomic signature of plasma cells producing abnormal Ig free light chains.

2020-05-14 | GSE119048 | GEO

Paired antibody heavy-light chain sequencing

Project description:Paired antibody heavy-light chain sequencing

| PRJEB25901 | ENA

Transcription elongation factor ELL2 influences splicing versus poly(A) site choice in the Ig heavy chain gene

Project description:Processing of Immunoglobulin heavy chain (IgH) mRNA is a paradigm for competition between splicing and polyadenylation. In plasma cells pre-mRNA is polyadenylated mainly at the promoter-proximal secretory site while B-cells utilize a cryptic 5’ splice site in the last secretory-specific exon; these are mutually exclusive events for all IgH pre-mRNAs. Transcription elongation factor ELL2, more abundant in plasma cells relative to B-cells, was down-modulated by overexpression of heterogenous ribonucleoprotein F, a condition which reduced production of secretory IgH mRNA. Transfection of B-cells with ELL2 and the IgH reporter showed an accelerated use of the secretory poly(A) site, positioned in competition with the splice to M1; a small interfering RNA to ELL2 reduced expression of IgH secretory mRNA. Co-transcription factors ELL1 and PC4 were ineffective at driving secretory-poly(A) site use. ELL2 had little effect on poly(A) site choice with reporters containing tandem-linked poly(A) sites. Shorter forms of ELL2 protein result from both internal initiation at M186 and protein processing. An alternative splicing reporter driven by IgH or non-Ig promoters revealed that ELL2 and its M186 initiated form were able to accelerate exon skipping. Therefore, ELL2 influences IgH pre-mRNA processing through facilitating skipping of the alternative splice to the membrane form.

2008-06-01 | GSE11586 | GEO

Single cell paired heavy- and light-chain immunoglobulin sequencing of sorted Lyme disease plasmablasts

Project description:Lyme disease (Borrelia burgdorferi infection) is increasingly recognized as a significant source of morbidity world-wide. Here, we investigated B cell responses to Lyme disease through barcode-enabled single cell sequencing of activated B cells (plasmablasts) sorted from PBMCs. Bulk immunglobulin heavy-chain sequencing from this project has also been separately deposited. Additional information regarding patient characteristics and overlap with other data from the SLICE study is available upon request.

2018-12-21 | GSE114309 | GEO

Heavy chain immunoglobulin sequencing of Lyme disease PBMCs

Project description:Lyme disease (Borrelia burgdorferi infection) is increasingly recognized as a significant source of morbidity world-wide. Here, we investigated B cell responses to Lyme disease through molecular identifier-enabled antibody heavy chain sequencing of bulk B cells from PBMCs. Single-cell immunoglobulin sequencing of paired heavy- and light-chain genes from this project will also be separately deposited. Additional information regarding patient characteristics and overlap with other data from the SLICE study is available upon request.

2018-12-21 | GSE113938 | GEO

Toxicity of LCDD monoclonal Ig free light chains on renal glomeruli

Project description:We analyzed the transcriptome (RNA-seq) of glomeruli in a mouse model of light chain deposition disease (LCDD) as compared to control mice (WT and DH-LMP2A, the latter producing no complete immunoglobulins, only free Ig light chains). Kidney lesions in LCDD are due to the deposition of an abnormal monoclonal free Ig light chain and comprise progressive thickening of basement membranes (tubular and glomerular) and nodular glomerulosclerosis resembling the lesions observed in diabetic nephropathy. The aim of the present study is to analyse the transcriptomic changes at early steps of glomerulosclerosis.

2020-05-14 | GSE119049 | GEO

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