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Transcriptomic analysis of naïve B cells and antigen-specific activated B cells and plasma cells from 4dpi NP-LPS immunized mice [NPLPS_PC]

ABSTRACT: Transcriptomic analysis of naïve B cells and antigen-specific activated B cells and plasma cells from 4dpi NP-LPS immunized mice [NPLPS_PC]

PROVIDER: PRJNA593427 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10584224.fastq.gz	Fastqsanger.gz
	SRR10584225.fastq.gz	Fastqsanger.gz
	SRR10584226.fastq.gz	Fastqsanger.gz
	SRR10584227.fastq.gz	Fastqsanger.gz
	SRR10584228.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis of naïve B cells and antigen-specific activated B cells and plasma cells from 4dpi NP-LPS immunized mice [NPLPS_PC]

Project description:Little is known about the earliest transcriptomic events in plasma cell differentiation. Indeed, activation of UPR-affiliated gene expression is seen in in-vitro plasma cell differentiation prior to Blimp1 upregulation and in the absence of Xbp1 as we show in linked companion series. In this study, Blimp1 reporter mice were immunized with the T-independent antigen NP-LPS four days prior to spleen harvest and naïve B cells, NP-binding activated B cells and NP-binding plasma cells were analyzed by bulk RNA-seq. Here we report the activation of ER remodeling gene expression in antigen-specific activated B cells in-vivo prior to upregulation of Blimp1 transcription.

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NP-18 vs. NP-18AR transcriptional profile upon treatment with TK/GCV

Project description:Pancreatic cancer-derived cells NP-18 underwent four rounds of treatment with increasing doses of an adenoviral vector encoding TK enzyme and GCV. Surviving cells were termed NP-18AR and displayed decreased sensitivity to treatment. This experiment analyses the transcriptomic effect of TK/GCV treatment on NP-18AR as compared to that of NP-18 cells. Two-condition experiment, where response to treatment in naïve cells (NP-18) was compared to response to treatment in previously treated resistant cells (NP-18AR). Biological replicates: samples from 3 independently generated and independently treated NP-18AR lines (NP-18AR1, NP-18AR2 and NP-18AR3) were hibridized with 3 independently treated samples of NP-18 cells. A total of 9 hybridizations were performed, 2 for NP-18AR1 (including 1 dye-swap), 4 for NP-18AR2 (including 2 dye swaps) and 3 for NP-18AR3 (including 1 dye-swap).

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Project description:To obtain insight into the genetic basis of the increase of functional activity of memory B cells over time, we compared the gene expression profiles of day 7 and day 40 NP-specific/IgG1 memory B cells, GC B cells and plasma cells in immunized WT mice and naïve B cells, before and after activation in vitro. Total RNAs in three replicates of NP-specific/IgG1 memory B cells, GC B cells and plasma cells in immunized WT mice at day 7 and 40 postimmunization and naïve follicular and marginal zone B cells, before and after activation in vitro, were amplified and labeled according to the Affymetrix's instructions. cRNA was hybridized to Mouse Genome 430 2.0 GeneChips (Affymetrix).

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Next generation sequencing of antibody heavy chain genes that bind to the hapten NP in sorted memory cells and long-lived plasma cells isolated from mice immunized orally with NP-CT

Project description:We report that there are differences in V gene usage in memory B cells and long-lived plasma cells after oral immunization. The hapten NP was conjugated to cholera toxin (CT) to create NP-CT, an antigen that is highly immunogenic after oral immunization. The NP hapten induces immune responses dominated by the 1-72 (VH186.2) heavy chain V region. The relationship between NP binding IgA antibody genes from memory B cells from spleen, MLN and Peyer´s patches and long-lived plasma cells from lamina propria and bone marrow that persisted 6-12 months after an oral immunization in three C57BL/6 mice with NP-CT was investigated. Extensive clonal overlap im clones was observed between long-lived memory cells from lamina propria and bone marrow, but very limited overlap was found between memory cells and plasma cells. The data suggest that memory and plasma cells formed through temporarily or anatomically separate processes.

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Single-cell profiling of the nucleus pulposus (NP) supports the Shh+ cells as NP stem cells

Project description:The physiological function of the intervertebral disc (IVD) depends on the cellular and molecular composition of the nucleus pulposus (NP), which plays a key role in managing the mechanical loading of the IVD.We conducted single-cell RNA sequencing (scRNA-seq) analysis to better characterize the NP cells, particularly the Shh-tdTom+ NP cells, in the adult Shh-CreER; Rosa26tdTomato mice.

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NP-18 vs. NP-18AR transcriptional profile upon treatment with TK/GCV

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