Mus musculus strain:SLC KO and C57BL/6
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA277306 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1841324.fastq.gz | Fastqsanger.gz | |||
| SRR1841327.fastq.gz | Fastqsanger.gz | |||
| SRR1840788.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:We report that B-1a cells develop in a surrogate light chain independent context. As a consequence, the precursor B-1a cell population avoids a pre-BCR positive selection stage. To confirm that the B-1a cells generated in this manner repersent a bonafide B-1a cell compartment, we did NGS on BCR rearrangements to assess the repertoire diversity. We find that as a whoile, B-1a cell repertoire that develop in Igll1 kncokout mice are similar compared to wild-type. This supports our findings that B-1a cells develop properly in the absence of surrogate light chain.
2018-01-15 | GSE104111 | GEO
Project description:Generation of the primary antibody repertoire requires V(D)J recombination of hundreds of gene segments in the immunoglobulin heavy chain (Igh) locus. It has been proposed that interleukin-7 receptor (IL-7R) signalling is necessary for Igh recombination, but this has been challenging to partition from the receptor’s role in B cell survival and proliferation. By generating the first detailed description of the Igh repertoire of murine IL-7Ra-/- bone marrow B cells, we demonstrate that IL-7R signalling profoundly influences VH gene selection during VH-to-DJH recombination. We find skewing towards usage of 3’ VH genes during de novo VH-to-DJH recombination that is more severe than the fetal liver (FL) B cell repertoire, and we now show a role for IL-7R signalling in DH-to-JH recombination. Transcriptome and accessibility analyses suggests reduced expression of B lineage-specific transcription factors (TFs) and their targets, and loss of DH and VH antisense transcription in IL-7Rα-/- B cells. These results refute models suggesting that IL-7R signalling is only required for survival and proliferation, and demonstrate a pivotal role in shaping the Igh repertoire by activating underpinning epigenetic mechanisms.
2021-02-20 | GSE157603 | GEO
Project description:Purpose: B-1a cells have a distinct BCR repertoire compared with that of B-2 cells. To examine whether CIC loss affects the BCR repertoire in B-1a cells, we analyzed mRNA sequences of immunoglobulin heavy (Igh) and light (Igk and Igl) chain genes in B-1a cells from 12-week-old control and Cicf/f;Cd19-Cre mice. Methods: Peritoneal cavity B-1a cells (IgM+, CD19+, CD5+, CD43+) were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. Long Read iR-Profile Reagent System (iRepertoire) was used to generate NGS libraries covering BCR chains including Igh, Igk, and Igl. Briefly, nested inside and outside primers selectively amplified all V- and C- regions and incorporated communal adaptors. Following clean up, only target amplicons, which contain 5’ and 3’ communal adaptors, were exponentially amplified. Amplified libraries were multiplexed for sequencing on the Illumina Miseq platform. Sequence reads were de-multiplexed according to the barcode sequences. Results: Trimmed reads were mapped to germline V, D and J reference sequences downloaded from the IMGT database. IgH diversity and the usage of variable (V) segments in heavy (Ighv) chain and light (Igkv and Iglv) chain genes were comparable between control and Cic-null B-1a cells. Analysis of non-templated (N)-nucleotide addition at V(D)J junctions revealed that Cic-null B-1a cells have a higher proportion of zero to two N-nucleotides-containing-BCRs than control cells. Conclusions: Our study presents the first comparative BCR repertoire analysis of wild-type and Cic-null B-1a cells. We concluded that CIC deficiency does not dramatically alter the BCR repertoire in B-1a cells.
2021-12-16 | GSE164147 | GEO
Project description:We studied the role of the stable Igh mRNA in Igh chain check point. Here we generated RNA-seq data from sorted ProB (CD19+B220+c-Kit+CD25-) and PreB (CD19+B220+c-Kit-CD25+) populations from Bone marrow of mice.
2020-12-29 | GSE144275 | GEO
Project description:By sequencing tens of millions of TCR? chain transcripts from naïve mouse CD8+ T cells, we observed a hugely diverse repertoire, comprising nearly all possible TRAV-TRAJ combinations. Our findings are not compatible with sequential coordinate gene recombination, but rather with a model in which contraction and DNA looping in the TCR?? locus provide equal access to TRAV and TRAJ gene segments, similar to that demonstrated for IgH gene recombination High-throughput sequencing of entire TCRa repertoire from C57Bl/6 mice
2012-02-09 | E-GEOD-35626 | biostudies-arrayexpress
Project description:In response to antigen challenge, human B cells clonally expand, undergo selection and differentiate within secondary lymphoid tissues to produce mature B cell subsets and high affinity antibodies necessary for an effective immune response. However, the interplay between affinity, antibody class and different B cell fates has proved challenging to decipher in primary human tissue. We have applied an integrated analysis of bulk and single-cell antibody repertoires paired with single-cell transcriptomics of human B cells from a model secondary lymphoid tissue. Specifically, here we have performed bulk B cell repertoire sequencing of the immunoglobulin heavy chain (IgH) for sorted B cell subsets from paediatric tonsil tissue. Matched single-cell gene expression and single-cell VDJ data are also available for the same patient donors.
2020-05-01 | E-MTAB-8999 | biostudies-arrayexpress
Project description:B cells are known to have different properties and BCR repertoires depending on the time of development. Our objective is to investigate the BCR repertoire of B cells across embryonic, neonatal, and adult stages, particularly in cells with a RAG2 expression history. We focus on sequencing and analyzing the immunoglobulin heavy chain (IGH) genes of these cells to understand their BCR diversity and specificity. Additionally, we explore the relationship between B-1a cells and bone marrow IgM+ plasmablasts/plasma cells, aiming to shed light on the development and function of B-1a cells in the immune system.
2023-12-17 | GSE250175 | GEO
Project description:Pre-B cell receptor (pre-BCR) signals initiate immunoglobulin light (Igl) chain gene assembly leading to RAG-mediated DNA double-strand breaks (DSBs). These signals also promote cell cycle entry, which could cause aberrant DSB repair and genome instability in pre-B cells. Here we show that RAG DSBs inhibit pre-BCR signals through the ATM- and NF-κB2-dependent induction of SPIC, a hematopoietic-specific transcriptional repressor. SPIC inhibits expression of the SYK tyrosine kinase and BLNK adaptor to prevent the pre-BCR from inducing additional Igl chain gene rearrangements and driving pre-B cells with RAG DSBs into cycle. We propose that pre-B cells toggle between pre-BCR signals and this RAG DSB-dependent checkpoint to maintain genome stability while iteratively assembling Igl chain genes. Three independent IL-7 cultures for each genotype (Rag1-/-:μIgH:Bcl2, Art-/-:μIgH:Bcl2 and Art-/-:Nfkb2-/-:μIgH:Bcl2) were withdrawn from IL-7 for 2 days. RNA was isolated using RNeasy (Qiagen). Gene expression profiling was performed using Illumina MouseRef-8 expression microarrays.
2016-01-13 | E-GEOD-67854 | biostudies-arrayexpress
Project description:We provide a novel gene fusion (ETV6-IgH) involving a truncation of ETV6 and leading to haploinsuffiency of ETV6 expression. ETV6-IgH is a new potential surrogate marker of PCNSL with favorable prognosis
2018-12-26 | GSE81816 | GEO
Project description:B cells reactive toward phosphatidylcholine (PtC) are enriched in the B1 B cell subset, and express predominantly one of two VH/Vk combinations to confer this specificity: VH12/Vk4/5H and VH11/Vk9. Studies of transgenic mice expressing the VH12 heavy chain (VH12 mice) suggest two major checkpoints for light chain expression in this system: the first involves selection of V-J rearrangements which encode a “permissive” light chain that can functionally pair with the VH12 heavy chain; the second involves receptor editing to salvage non-PtC reactive B cells to acquire a permissive light chain that confers PtC reactivity. If this model is correct, impairing receptor editing should reduce the frequency of PtC-reactive B1 B cells in VH12 mice. To test this possibility, we bred VH12 mice to transgenic mice expressing a catalytically inactive form of RAG1 (dnRAG1 mice) which show a defect in receptor editing. Interestingly, dnRAG1 expression in VH12 mice enforces development of PtC-reactive B1 B cells, rescuing the loss of splenic B cells observed in VH12 mice. These data suggest receptor editing normally functions to remove a large portion of PtC-specific B cells in VH12 mice. Deep sequencing of the expressed light chain repertoire of PtC-reactive and non-reactive B cells in VH12 mice revealed that PtC-reactive B cells predominantly expressed the Vk4/5H (IGKV4-91) light chain gene, whereas PtC-non-reactive B cells expressed a broader, yet restricted, set of light chain genes. This analysis also revealed a low frequency of in-frame hybrid light chain genes appearing to originate via Type 2 gene replacement, which we show can originate from template switching during PCR.
2022-06-01 | GSE165776 | GEO