GEO DataSets

(Submitter supplied) Antibody class switch recombination (CSR) in B lymphocytes joins two DNA double-strand breaks (DSBs) lying 100 to 200 kilobases (kb) apart within switch (S) regions in the immunoglobulin heavy chain locus (IgH). CSR-activated B lymphocytes generate multiple S-region DSBs in the donor Sm and in a downstream acceptor S region, with a DSB in Sm being joined to a DSB in the acceptor S region at sufficient frequency to drive CSR in a large fraction of activated B cells. more...

Organism:

Mus musculus

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL16417

13 Samples

Download data: TXT

(Submitter supplied) During B cell development, RAG endonuclease cleaves immunoglobulin heavy chain (IgH) V, D, and J gene segments and orchestrates their fusion as deletional events that assemble a V(D)J exon in the same transcriptional orientation as adjacent Cμ constant region exons. In mice, six additional sets of constant region exons (CHs) lie 100-200kb downstream in the same transcriptional orientation as V(D)J and Cμ exons. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

122 Samples

Download data: TXT

(Submitter supplied) IgH class switch recombination (CSR) in B lymphocytes switches IgH constant regions to change antibody functions. CSR is initiated by DNA double strand breaks (DSBs) within a donor IgH switch (S) region and a downstream acceptor S region. CSR is completed by fusing donor and acceptor S region DSB ends by classical non-homologous end-joining (C-NHEJ) and, in its absence, by alternative end-joining (A-EJ) that is more biased to use longer junctional micro-homologies (MHs). more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

48 Samples

Download data: XLS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL16417 GPL21626

149 Samples

Download data: BEDGRAPH, BROADPEAK, BW, TXT

(Submitter supplied) In a B lymphocyte immunoglobulin heavy chain locus (IgH), a developmentally assembled V(D)J exon encoding an antibody variable region lies upstream of exons encoding a m constant region (Cm), allowing generation of mIgH chain transcripts and IgM-class antibodies1. Mouse IgH class switch recombination (CSR) replaces Cmwith one of 6 sets of constant region exons (CHs) that lie 100-200kb downstream1. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21626

22 Samples

Download data: BW

(Submitter supplied) In a B lymphocyte immunoglobulin heavy chain locus (IgH), a developmentally assembled V(D)J exon encoding an antibody variable region lies upstream of exons encoding a  constant region (C), allowing generation of IgH chain transcripts and IgM-class antibodies1. Mouse IgH class switch recombination (CSR) replaces Cwith one of 6 sets of constant region exons (CHs) that lie 100-200kb downstream1. more...

Organism:

Mus musculus

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL16417

21 Samples

Download data: TXT

(Submitter supplied) In a B lymphocyte immunoglobulin heavy chain locus (IgH), a developmentally assembled V(D)J exon encoding an antibody variable region lies upstream of exons encoding a  constant region (C), allowing generation of IgH chain transcripts and IgM-class antibodies1. Mouse IgH class switch recombination (CSR) replaces Cwith one of 6 sets of constant region exons (CHs) that lie 100-200kb downstream1. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

31 Samples

Download data: BROADPEAK, BW

(Submitter supplied) In a B lymphocyte immunoglobulin heavy chain locus (IgH), a developmentally assembled V(D)J exon encoding an antibody variable region lies upstream of exons encoding a m constant region (Cm), allowing generation of mIgH chain transcripts and IgM-class antibodies1. Mouse IgH class switch recombination (CSR) replaces Cmwith one of 6 sets of constant region exons (CHs) that lie 100-200kb downstream1. more...

Organism:

Mus musculus

Type:

Genome variation profiling by high throughput sequencing

Platforms:

GPL16417 GPL21626

75 Samples

Download data: BEDGRAPH

(Submitter supplied) High-throughput genome-wide translocation sequencing (HTGTS) is a robust approach to identify genome-wide translocation junctions. We performed HTGTS to study the fate of introduced c-myc DSBs in mouse splenic B cells activated for activation cytidine deaminase (AID)-dependent class switch recombination (CSR). We found frequent translocations of c-myc DSBs to AID-initiated DSBs in IgH switch regions in wild-type (WT) and ATM-deficient B cells. more...

Organism:

Mus musculus

Type:

Other

Platforms:

GPL16417 GPL16815

16 Samples

Download data: TXT

(Submitter supplied) We performed CSR-HTGTS-Seq, 3C-HTGTS, GRO-Seq and ChIP-Seq in mature splenic B cells with different stimulation study physiological roles of 3'CBEs in antibody class switching

Organism:

Mus musculus

Type:

Other

Platform:

GPL21626

18 Samples

Download data: BW

(Submitter supplied) We performed CSR-HTGTS-Seq, 3C-HTGTS, GRO-Seq and ChIP-Seq in mature splenic B cells with different stimulation study physiological roles of 3'CBEs in antibody class switching

Organism:

Mus musculus

Type:

Other

Platform:

GPL21626

12 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Other

Platform:

GPL21626

42 Samples

Download data: BEDGRAPH, BW, TXT

(Submitter supplied) We performed CSR-HTGTS-Seq, 3C-HTGTS, GRO-Seq and ChIP-Seq in mature splenic B cells with different stimulation study physiological roles of 3'CBEs in antibody class switching

Organism:

Mus musculus

Type:

Other

Platform:

GPL21626

12 Samples

Download data: TXT

(Submitter supplied) During Class Switch Recombination (CSR) B cells replace the Igh Cμ/δ exons with another downstream constant region exon (CH), altering the antibody isotype. CSR occurs through the introduction of AID-mediated double strand break (DSBs) in switch regions and subsequent ligation of broken ends. Here we developed an assay to investigate the dynamics of DSB introduction in individual cells. We demonstrate that the upstream switch region Sμ is always targeted first during recombination and that the mechanism underlying this control relies on 53BP1. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

13 Samples

Download data: BEDGRAPH

(Submitter supplied) Activation-induced deaminase (AID) is the major actor of immunoglobulin (Ig) genes diversification in germinal center B cells. From its first description, it was considered as mandatory for class switch recombination (CSR) and this discovery initiated a long quest for all of the AID-interacting factors controlling its activity. The mechanisms focusing AID-mediated DNA lesions to given target sequences remain incompletely understood, with regards to the detailed characterization of optimal substrates in which cytidine deamination will lead to double strand breaks (DSBs) and chromosomal cleavage. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL25723 GPL23934

23 Samples

Download data: XLSX

(Submitter supplied) These tracks include chromatin interaction data produced using the 5C (chromatin conformation capture carbon copy) method by the Kenter Lab located at the University of Illinois College of Medicine, Chicago, IL. These tracks show looping interactions across the Igh locus using alternating forward and reverse primer design scheme. The 3C method uses formaldehyde crosslinking to covalently associate interacting chromatin segments in intact cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL9250

2 Samples

Download data: TXT

(Submitter supplied) These tracks include chromatin interaction data produced using the 5C (chromatin conformation capture carbon copy) method by the Kenter Lab located at the University of Illinois College of Medicine, Chicago, IL. These tracks show looping interactions across the Igh locus using alternating forward and reverse primer design scheme. The 3C method uses formaldehyde crosslinking to covalently associate interacting chromatin segments in intact cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL9250

2 Samples

Download data: TXT

(Submitter supplied) We report the application of 4C-seq for analysis of the 3’ end of he Igh locus during B cell development. We generated genome-wide 4C maps for BM derived Rag2-/- pro-B cells, resting splenic B cells, LPS+IL4 activated B cells and ConA stimulated splenic T cells using two viewpoints, Em and hs4 located in 3’Ea. We find that long range interactions are present only on B lineage cells reflecting enhancer activation status.

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

16 Samples

Download data: WIG

(Submitter supplied) Memory B cells (MBCs) are long-lived and rapidly respond to cognate antigen with production of high-affinity, generally, class-switched antibodies. Here, we have developed an integrative analysis of differentially expressed (DE) mRNAs, miRNAs, lncRNAs, chromatin profiles and cis-regulatory elements to determine how gene expression intersects with epigenetic regulatory elements in human MBCs. Using a multiparameter cell sorting approach, we isolated CD27-IgD+NBCs, CD27+IgD+unswMBCs, CD27+IgG+swMBCs and CD27+IgA+swMBCs as well as total CD27-NBCs and CD27+MBCs from peripheral blood of healthy human subjects of different age, sex and ethnic background. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20301

40 Samples

Download data: TXT

(Submitter supplied) To generate antibodies with different effector functions, B cells undergo Immunoglobulin class switch recombination (CSR). The ligation step of CSR is usually mediated by the classical non-homologous end-joining (cNHEJ) pathway. In cNHEJ-deficient cells, a remarkable ~25% CSR can be achieved by the alternative end-joining (A-EJ) pathway that preferentially uses microhomology (MH) at the junctions. While A-EJ mediated repair of endonuclease generated breaks requires DNA end-resection, we show that CtIP-mediated DNA end-resection is dispensable for A-EJ-mediated CSR using cNHEJ-deficient B cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

42 Samples

Download data: XLSX