Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-seq of OT-I cells co-cultured with vehicle or TAMos under OVA257-264 stimulation

ABSTRACT: To characterize the regulation of tumor-associated monocytes (TAMos) on the epigenetic map of T cells, we conducted the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) of OT-I cells co-cultured with vehicle or TAMos derived from the spleens of LLC tumor-bearing mice in response to OVA257-264 peptides.

ORGANISM(S): Mus musculus

PROVIDER: GSE224872 | GEO | 2026/02/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq of OT-I cells co-cultured with vehicle, TANs or TAMos under OVA257-264 stimulation

Project description:To explore the effects of tumor-associated monocytes (TAMos) on T cell transcriptional landscape, we conducted RNA transcriptome profiling of OT-I cells co-cultured with vehicle, tumor-associated neutrophils (TANs), or TAMos derived from the spleens of LLC tumor-bearing mice in response to OVA257-264 peptides.`

2026-02-07 | GSE224871 | GEO

ATAC-seq of OT-I cells co-cultured with vehicle or TAMos under OVA257-264 stimulation

Project description:ATAC-seq of OT-I cells co-cultured with vehicle or TAMos under OVA257-264 stimulation

| PRJNA932825 | ENA

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

RNA-seq of OT-I cells co-cultured with vehicle, TANs or TAMos under OVA257-264 stimulation

Project description:RNA-seq of OT-I cells co-cultured with vehicle, TANs or TAMos under OVA257-264 stimulation

| PRJNA932823 | ENA

Single-cell RNA sequencing of OT-I CD8+ T cells after stimulation with different affinity ligands

Project description:Activation of CD8+ T cells depends exquisitely on the affinity of the T cell receptor (TCR) for a peptide MHC (pMHC) ligand complex. Here, we activated OT-I transgenic CD8+ T cells with pure peptide and examined early activation responses by single-cell RNA-sequencing. T cells were activated with the high affinity OT-I cognate peptide (N4=SIINFEKL) for 1, 3 or 6 hours, or with reduced affinity peptides (T4=SIITFEKL and G4=SIIGFEKL) or the non-binding peptide (NP68=ASNENMDAM) for 6 hours. Cells were then sorted into 96-well plates by FACS and RNA was sequenced following an adapted Smart-Seq2 protocol.

2018-06-25 | E-MTAB-6051 | biostudies-arrayexpress

Time-resolved phosphoproteomic analysis of murine CD8+ T cells upon stimulation with ligands of different affinity to the TCR

Project description:T cells have the remarkable ability to sense and discriminate between a wide range of antigenic peptides bound to major histocompatibility complex molecules (pMHC). Here, we use phosphoproteomics to monitor in a time dependent manner the signalling cascade taking place upon stimulation of murine CD8+ T cells with ligands of different affinity to the TCR. We used the mouse OT-I model in which T cells specifically recognize the ovalbumin OVA257-264 peptide (SIINFEKL, also named N4) bound to the MHC-I molecule H-2Kb (pMHC). The OT-I TCR also recognizes altered peptide ligands amongst which SIITFEKL (T4) and SIIGFEKL (G4) with sub-optimal binding capacities (ligand affinity N4>T4>G4). CD8+ T cells were purified from pooled lymph nodes and spleens, shortly expanded, and were left unstimulated or stimulated with N4, T4 and G4 soluble pMHC tetramers for 30, 120, 300 or 600s. We conducted six independent multiplexed experiments, each containing either independent stimulations with the N4 and T4 peptides (N4-T4 experiments, 3 replicates) or with the N4 and G4 peptides (N4-G4 experiments, 3 replicates). Samples from each experiment were labeled by TMT10plex, pooled and subjected to phospho-enrichment using first TiO2 beads and then phospho-Tyrosine (pY) immuno-precipitation (IP). Samples were injected before TiO2 enrichment, after TiO2 and after TiO2 followed by pY IP for analysis of the proteome, serine/threonine phospho-proteome and tyrosine phospho-proteome, respectively.

2022-07-05 | PXD030080 | Pride

Analysis of the interactomes of ZAP70, CD247 and SLP76 upon stimulation of murine CD8+ T cells with ligands of different affinity to the TCR

Project description:T cells have the remarkable ability to sense and discriminate between a wide range of antigenic peptides bound to major histocompatibility complex molecules (pMHC). Here, we use interactomics to monitor in a time dependent manner the early molecular events taking place upon stimulation of murine CD8+ T cells with ligands of different affinity to the TCR. We used the mouse OT-I model in which T cells specifically recognize the ovalbumin OVA 257-264 peptide (SIINFEKL, also named N4) bound to the MHC-I molecule H-2Kb (pMHC). The OT-I TCR also recognizes altered peptide ligands amongst which SIITFEKL (T4) and SIIGFEKL (G4) with sub-optimal binding capacities (ligand affinity N4>T4>G4). For affinity purification (AP) of signalling complexes, we crossed OT-I TCR transgenic mice onto mice expressing an endogenous tagged (One-Strep-Tag: OST) version of the CD3z (also called CD247), ZAP70 or SLP76 molecules. CD8+ T cells were purified from pooled lymph nodes and spleens, shortly expanded, and were left unstimulated or stimulated with N4, T4 and G4 soluble pMHC tetramers for 30, 120 or 300 s. Complexes formed around either CD247, ZAP70 or SLP76 were then purified and analysed by mass spectrometry. Each AP-MS purification is associated with a corresponding control (purification from OT-I CD8+ T cells expressing only the endogenous version of each bait, cultured and stimulated in the same conditions). The number of replicate biological experiments was n=3 for all time-points, and each sample was analyzed twice by single-run nano LC-MS. In addition, the whole proteome of OT-I cell was analyzed by label-free shotgun proteomics in order to calculate cellular protein abundances for each interactor.

2022-07-05 | PXD029974 | Pride

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 naïve 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.

2013-12-10 | GSE53200 | GEO

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

Desulfosporosinus sp. OT strain:OT

Project description:Desulfosporosinus sp. OT genome sequencing

| PRJNA61253 | ENA