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Positive and Negative Selection of abT cells (OT-I and OT-II) in the thymus 2 - scRNA-seq, CITE-seq and TCRab

ABSTRACT: This study is part of the immgenT Open Source Project, specifically IGT59, which characterizes activated CD4 and CD8 T cells in the spleen and brain during Toxoplasma gondii infection at 9 dpi (peak infection in the spleen) and 23 dpi (chronic phase with brain cysts). Splenocytes from uninfected controls were also profiled. It includes a spleen control at baseline (6-8-week-old C57BL/6J mouse).

ORGANISM(S): Mus musculus

PROVIDER: GSE330985 | GEO | 2026/05/19

REPOSITORIES: GEO

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Spleen and brain T cells in Toxoplasma gondii infection- scRNA-seq, CITE-seq and TCRab

Project description:This study is part of the immgenT Open Source Project, specifically IGT59, which characterizes activated CD4 and CD8 T cells in the spleen and brain during Toxoplasma gondii infection at 9 dpi (peak infection in the spleen) and 23 dpi (chronic phase with brain cysts). Splenocytes from uninfected controls were also profiled. It includes a spleen control at baseline (6-8-week-old C57BL/6J mouse).

2026-05-18 | GSE330911 | GEO

Positive and Negative Selection of abT cells (OT-I and OT-II) in the thymus 1 -scRNA-seq, CITE-seq and TCRab

Project description:This study is part of the immgenT Open Source Project, specifically from IGT58, focuses on the positive and negative selection of OT1 and OT2 in the thymus. Bone marrow chimeras were generated by transplanting OT1 or OT2 CD45.1.2 and wild-type competitor BM into wild-type, RIPmOVA, B2m -/- or MHCII -/- hosts. From those mice, OT1 and OT2, not selected, positively selected, or negatively selected, were profiled.

2026-05-18 | GSE330896 | GEO

T cells in B16 tumor model with ACT and checkpoint blockade - scRNA-seq, CITE-seq and TCRab [i35]

Project description:This study is part of the immgenT Open Source Project, specifically from IGT35, which focuses on characterizing T cells in the B16.gp33 melanoma model following adoptive cell therapy (ACT) and immune checkpoint blockade. T cells were isolated from tumors and draining inguinal lymph nodes of C57BL/6J male mice (7–8 weeks old) subjected to subcutaneous implantation of B16.gp33 melanoma cells, followed by adoptive cell transfer treatment with intravenous transfer of P14 and pmel T cells, and treatment with either isotype control antibodies or a combination of anti-PD-1 and anti-4-1BB antibodies. Samples were collected at day 14 post post-tumor implantation (1 day post-final antibody treatment). The study targeted all CD3+ T cell populations, including transgenic P14 and pmel T cells

2025-12-01 | GSE311344 | GEO

OT-I T cell activation in Lrrc8af/f and Lrrc8af/f Cd4-Cre;OT-I mice

Project description:Splenocytes were separated from Lrrc8af/f and Lrrc8af/f Cd4-Cre;OT-I mice. The splenocytes were stimulated with indicated peptides (unstime/ SIINFEKL-10pM(NL)/ SIINFEKL-1000pM(NH)/ SIIGFEKL-1000nM(G4)) for 6 hours. The OT-I CD8+ T cells were labeled with Va2-PE/CD8-A700 and sorted for the sequencing.

2023-09-26 | GSE243985 | GEO

Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 60) [I40]

Project description:This study is part of the immgenT Open Source Project, specifically from IGT40, which focuses on a pan-organ and time course analysis of T cells in acute LCMV (Armstrong) infection at day 60 post-infection. The dataset includes T cells isolated from multiple organs: spleen, prostate, submandibular gland, bone marrow, mesenteric lymph node, small intestine epithelium, small intestine lamina propria, lung, and mediastinal lymph node. 7-week-old male C57BL/6J mice infected intraperitoneally with 2×10^5 PFU LCMV Armstrong, and T cells were analyzed at 60 days post-infection (dpi). The study includes both endogenous T cells and adoptively transferred P14 and SMARTA TCR transgenic T cells. Mice received IV 100,000 SMARTA (CD45.1.2) and 50,000 P14 (CD45.1) T cells one day before infection.

2025-08-19 | GSE301961 | GEO

Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7) [I36]

Project description:This study is part of the immgenT Open Source Project, specifically from IGT36, which focuses on a pan-organ and time course analysis of T cells in acute LCMV (Armstrong) infection at day 7 post-infection. The dataset includes T cells isolated from multiple organs: spleen, prostate, submandibular gland, bone marrow, mesenteric lymph node, small intestine epithelium, small intestine lamina propria, lung, and mediastinal lymph node. 7-week-old male C57BL/6J mice infected intraperitoneally with 2×10^5 PFU LCMV Armstrong, and T cells were analyzed at 60 days post-infection (dpi). The study includes both endogenous T cells and adoptively transferred P14 and SMARTA TCR transgenic T cells. Mice received IV 100,000 SMARTA (CD45.1.2) and 50,000 P14 (CD45.1) T cells one day before infection.

2025-08-19 | GSE301271 | GEO

Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 30) [I38]

Project description:This study is part of the immgenT Open Source Project, specifically from IGT38, which focuses on a pan-organ and time course analysis of T cells in acute LCMV (Armstrong) infection at day 30 post-infection. The dataset includes T cells isolated from multiple organs: spleen, prostate, submandibular gland, bone marrow, mesenteric lymph node, small intestine epithelium, small intestine lamina propria, lung, and mediastinal lymph node. 7-week-old male C57BL/6J mice infected intraperitoneally with 2×10^5 PFU LCMV Armstrong, and T cells were analyzed at 60 days post-infection (dpi). The study includes both endogenous T cells and adoptively transferred P14 and SMARTA TCR transgenic T cells. Mice received IV 100,000 SMARTA (CD45.1.2) and 50,000 P14 (CD45.1) T cells one day before infection.

2026-03-23 | GSE301960 | GEO

Temporal analysis of in vivo Toxoplasma gondii cysts shows novel and late stage specific transcripts.

Project description:The protozoan pathogen Toxoplasma gondii has the unique ability to develop a chronic infection in the brain of its host. The T. gondii develops cysts within the neurons that are resilient against the host immune response and current therapeutics. The bradyzoite parasites within the cyst have a sugar-protein-rich wall and a slow-replication cycle, allowing them to remain hidden from the host. This intracellular encysted lifestyle of T. gondii has made them recalcitrant to molecular analysis in vivo. Here, we have enriched for T. gondii brain cysts 21 to 150 days post-infection (DPI). RNA and protein from bradyzoites was isolated from each timepoint. Deep sequencing of transcripts expressed during these three timepoints showed many of the identified proteins are transcriptionally expressed at a high level. Approximately one-third are more enriched during bradyzoite conditions compared to tachyzoites, and approximately half are expressed at similar levels during each phase. We have expanded the transcriptional profile of in vivo bradyzoites to 120 DPI. The RNA sequencing depth of in vivo bradyzoite T. gondii was over 250-fold greater than was have been previously, which allowed us to identify low level transcripts and novel bradyzoite-specific isoforms.

2019-07-11 | GSE134099 | GEO

CITE-seq of SUMOi treated C57Bl6 mice

Project description:In our study, we investigated the effect of inhibition of SUMOylation on murine splenocytes. Mice were treated with 7,5 mg/kg SUMOi (TAK-981) on day 1 and day 4 and analysed on day5.

2022-01-15 | GSE193359 | GEO

Responses to SARS-CoV-2 variants in hACE2 transgenic mice

Project description:hACE2 transgenic mice were infected with the original SARS-CoV-2 strain (B.1) and the Beta (B.1.351) variant. Lung and spleen samples were collected 1 day post infection (DPI), 3 DPI and 5 DPI, and mRNA was sequenced.

2023-09-22 | E-MTAB-13308 | biostudies-arrayexpress

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