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Next Generation Sequencing of CNS-infiltrating Tox-sufficient and -deficient OT-1 cells in ODC-OVA mice 7 days after LCMV-OVA infection

ABSTRACT: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to compare the transcriptome of CNS-infiltrating OT-1 WT and Tox-deficient cells during effector phase (7 days after infection with LCMV-OVA)

ORGANISM(S): Mus musculus

PROVIDER: GSE93804 | GEO | 2018/05/17

REPOSITORIES: GEO

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Next Generation Sequencing of splenic- and CNS-infiltrating OT-1 cells in ODC-OVA mice upon LCMV-OVA and Lm-OVA infection

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to compare the transcriptome of OT-1 cells during priming (3 days after infection) and during effector phase ( 7 days after infection) in ODC-OVA mice after LCMV-OVA and Lm-OVA infection

2018-05-17 | GSE93805 | GEO

Bulk RNAseq of OT-1 T cells in OVA-pregnant and OVA-grafted mice

Project description:Purpose: The molecular circuits which govern CD8 T cell fate after alloimmunization by transplantation or pregnancy are unknown. The goals of this study are to perform whole transcriptome profiling (RNA-seq) of antigen-experienced CD8 T cells in parous and grafted mice to determine whether these cells become memory or exhausted T cells. Methods: mRNA profiles of OT-1 T cells recovered fom naive,OVA-skin grafted and OVA-parous mice were generated by bulk RNA-sequencing. OT-1 cells were FACS sorted from 10 individual mice per each of the three groups and then pooled together into three replicate samples per group. The sequence reads that passed quality filters were analyzed after aligning (STAR) with EdgeR. Results: Comparison of OT-1 T cells from OVA-grafted and OVA-parous mice revealed 400 differentially expressed genes. Conclusions: Skin grafting promotes the differentiation of canonical memory CD8 T cells whereas pregnancy promotes the differentiation of exhausted CD8 T cells with diminished recall capacity.

2021-12-06 | GSE188808 | GEO

TCR beta sequencing of blood and tumor samples from EG7.OVA bearing wildtype mice with OT-1 T cell transfer

Project description:We report the application of TCRβ sequencing to understand T cell repertoire of matched blood and tumor samples pre and post treatment in EG7.OVA tumor bearing mice with OT-1 cell transfer. TCRβ sequencing demonstrated that OT-1 (CASSRANYEQYF) was the most abundant T-cell clone in both blood and tumors of mRBC‑OVA-4-1BBL-IL-12 treated mice. To investigate the effects of mRBC‑OVA-4-1BBL-IL-12 on immune memory, the T cell repertoire was also analyzed before and after EG7.OVA and EL4 tumor rechallenge in cured and treatment-naive mice. TCRβ sequencing on T cells in peripheral blood showed that OT-1 clones increased in frequency after EG7.OVA challenge in previously cured mice. OT-1 frequency did not increase in treatment-naïve mice after tumor challenge, indicating that the tumor alone is insufficient to drive OT-1 cell expansion. We also evaluated the frequencies of unique TCRβ sequences in T cell clones that significantly expanded post EL4 challenge (EL4 responsive TCR). Increased frequency of EL4-responsive TCRs upon each tumor challenge (EG7.OVA and EL4) was associated with complete responders (mice that rejected EL4 challenge), suggesting that T-cell-mediated protection against parental tumor antigens was generated prior to EL4 challenge. Partial responders (delayed tumor growth compared with naïve mice) had increases in EL4-responsive TCR frequencies after EL4 challenge but not during the EG7.OVA rechallenge, whereas the non-responder (tumor growth similar to naïve mice) had minimal increases in TCR frequencies upon EL4 challenge. Overall, the ability to control EL4 tumors correlated with the expansion of EL4-responsive TCR clones.

2021-03-13 | GSE168826 | GEO

Bulk RNAseq of OT-1 T cells in OVA-pregnant and OVA-grafted mice

Project description:Bulk RNAseq of OT-1 T cells in OVA-pregnant and OVA-grafted mice

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RNA-sequencing of BCL6-sufficient and -insufficient OT-II TFH cells

Project description:We analyzed the transcriptome differences of BCL6-sufficient (CD4-Cre) and -insufficient (CD4-CrexBcl6fl/+) OT-II TFH cells. CD4-CrexBcl6fl/+ or control CD4-Cre OT-II T cells were transferred into CD45.1 Sap-/- mice. At day 3 post NP-OVA immunization, CXCR5hiPD-1hi TFH cells were sort-purified from the draining lymph node and prepared for RNA-seq analysis. Two technical repeats of ~200 cells per sample from each of 3 mice were included. BCL6-insufficient TFH cells differentially expressed many genes; among those downregulated were Stim1 and Plcg1, which code for STIM1 and PLCg1, respectively, that both impinge on calcium signaling downstream of TCR activation. Moreover, KEGG pathway analyses revealed that the calcium signaling-related pathway was generally upregulated in wildtype as compared to BCL6-insufficient TFH cells. These data support the notion that BCL6 control follicular T-B interactions by regulating multiple target genes involved in antigen-triggered calcium signaling in T cells.

2021-07-30 | GSE180924 | GEO

RNA-seq of Tfh cells from BALB/c and C57Bl/6 mice immunized with OVA-IFA or OVA-CpG

Project description:The aim of the project was the identification of the transcriptional signature of effector T cells and Tfh cells that emerge following immunization with different adjuvants. For this purpose OVA-specific TCR-transgenic cells (from DO11.10 or OT-II mice) were adoptively transferred into congenic BALB/c or C57Bl/6 mice, subsequently immunized with OVA-IFA or OVA-CpG. At day 11, the OVA-specific T effector and Tfh cells were FACS sorted from the draining lymph nodes for RNA sequencing.

2023-04-15 | E-MTAB-12086 | biostudies-arrayexpress

Gene expression in adoptively transferred OT-II cells isolated from mesenteric lymph nodes of control or MHCIIB-/- chimeras 5 days post-immunization with OVA and polyI:C.

Project description:To gain insight into the transcriptional program conferred to Th cells by B cells, we conducted microarray gene expression analyses of adoptively transferred OT-II cells sorted from the mesenteric lymph nodes of bone marrow chimeric control and MHCIIB-/- mice 5 days after immunization with OVA and polyI:C.

2021-11-11 | E-MTAB-11165 | biostudies-arrayexpress

RNA sequencing of wild type and FXR KO CD8+T cells in fed/fasted LCMV-infected mice

Project description:Conditional ablation of FXR in T cells was achieved with CD4-Cre Nr1h4fl/fl mice. Twenty thousend congenically marked naive (CD44- CD62L+) WT and FXR KO T cells carrying the OT-I transgenic TCR were cotransferred into lymphoreplete hosts. Recipients were challenged with LCMV-OVA and allowed to feed Ad libitum (AL) or fasted (Fs) for 24h beginning at 6pm on D5 post-infection. Splenic CD44+ effector cells of each genotype were FACS-purified (double-sorted) at the end of the starvation period.

2020-12-04 | GSE157439 | GEO

FcgRIIB+ and FcgRIIB- OT-I T cells d14 post OVA skin graft

Project description:FcgRIIB+ and FcgRIIB- OT-I T cells d14 post OVA skin graft

| PRJNA485651 | ENA

Expression data from OT-I CD8 T cells activated with DC in the presence or absence of CpG-Induced Inflammation

Project description:Inflammatory cytokines promote the accumulation of activated CD8 T cells. Here, we transfer 600 OT-I CD8 T cells iv into naÃ¯ve C57BL/6 hosts. One day later, 500,000 LPS-matured and OVA257 peptide-coated DC were injected iv into OT-I CD8 T cell seeded hosts with (DC+CpG) or without (DC). Other seeded mice were infected with 2x10^4 virulent Listeria monocytogenes (vLM-OVA) iv. OT-I CD8 T cells were harvested from the spleen, flow sort purified, then RNA was extracted using RNeasy (Qiagen) kit. Naive OT-I CD8 T cells (Naive) were purified from the spleens of OT-I transgenic mice. Each group had three independent biological replicates.Transcriptomes were compared using DAVID analysis (with genes scoring FDR<0.01) and GSEA analysis. 3 biological replicates per group. Groups included NaÃ¯ve OT-I CD8 T cells, DC+CpG OT-I CD8 T cells, DC OT-I CD8 T cells, and vLM-OVA OT-I CD8 T cells. Most comparisons used NaÃ¯ve OT-I CD8 T cells as a baseline comparison

2013-12-10 | E-GEOD-53200 | biostudies-arrayexpress

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