Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell TCR-seq of T cells isolated from MC38 mouse tumors

ABSTRACT: We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Tumors were taken one day after group-out (average 150-250 mm3 at day 0), approximately 14-19 days. Tissues were dissociated and flow sorted accordingly to obtain the following groups for 10x Chromium 5' Gene Expression Profiling. Our results indicate that the degree of clonal expansion is correlated with expression of T cell exhaustion markers, and that T cells with strong exhaustion phenotype also express high levels of activation markers, such as interferon gamma.

INSTRUMENT(S): Illumina HiSeq 2500, Compute Cluster

ORGANISM(S): Mus musculus

SUBMITTER: Soren Muller

PROVIDER: E-MTAB-7918 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA-seq profiling of T cells isolated from MC38 mouse tumors

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Tumors were taken one day after group-out (average 150-250 mm3 at day 0), approximately 14-19 days. Tissues were dissociated and flow sorted accordingly to obtain the following groups for 10x Chromium 5' Gene Expression Profiling. Our results indicate that the degree of clonal expansion is correlated with expression of T cell exhaustion markers, and that T cells with strong exhaustion phenotype also express high levels of activation markers, such as interferon gamma.

2019-05-12 | E-MTAB-7919 | biostudies-arrayexpress

Single cell TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Draining lymph nodes were taken one day after group-out (average 150-250 mm3 tumor size at day 0), approximately 14-19 days. Draining lymph nodes were dissociated and flow sorted accordingly to obtain the cells for 10x Chromium 5' Gene Expression Profiling and TCR sequencing.

2022-08-16 | E-MTAB-9734 | biostudies-arrayexpress

Single cell RNA-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Draining lymph nodes were taken one day after group-out (average 150-250 mm3 tumor size at day 0), approximately 14-19 days. Draining lymph nodes were dissociated and flow sorted accordingly to obtain the cells for 10x Chromium 5' Gene Expression Profiling.

2021-02-16 | E-MTAB-9274 | biostudies-arrayexpress

Single-cell RNAseq of CD45 positive cells in MC38 tumors - Primary irradiated tumors and secondary non-irradiated tumors - Concurrent treatment with anti-PD-L1

Project description:Primary irradiated MC38 tumors and secondary MC38 non-irradiated tumors. Subcutaneous MC38 tumors in C57BL/6 mice Concurrent treatment with anti-PD-L1.

2023-10-15 | E-MTAB-13389 | biostudies-arrayexpress

Single-cell RNA-seq of MC38 tumor model

Project description:Single-cell RNA-seq was performed on CD45+ and T cells sorted from MC38 tumors from mice.

2024-12-06 | E-MTAB-14590 | biostudies-arrayexpress

scRNA-seq and scTCR-seq of tetramer-positive T cells from IL27 treated tumor bearing mice

Project description:To characterize the consequences of systemic IL-27R agonism via IL-27 overexpression or IL-27 blockade (αIL-27) on anti-tumor CTL, we performed scRNA-seq of M86 neoantigen-specific CD8+ T cells from MC38 tumors and dLN.

2024-12-05 | E-MTAB-14601 | biostudies-arrayexpress

Somatic Gain-of-Function mTOR mutation in Clonally Expanded T-lymphocytes Associated with Chronic Graft-Versus-Host Disease

Project description:Graft-versus-host-disease (GvHD) is the main complication of allogeneic hematopoietic stem cell transplantation (HSCT). Here we report studies of a patient with chronic GVHD (cGVHD) carrying persistent CD4+ T cell clonal expansion which harbored somatic mTOR, NFKB2, and TLR2 mutations. Functional analysis of the discovered mTOR mutation indicated a gain-of-function alteration and activation of both mTORC1 and mTORC2 signaling pathways leading to increased cell proliferation and decreased apoptosis. Single-cell RNA sequencing and real-time impedance measurements supported increased cytotoxicity of mutated CD4+ T cells. High throughput drug-sensitivity testing suggested mutations induce resistance to mTOR inhibitors but increase sensitivity for HSP90 inhibitors. Our findings suggest that somatic mutations may contribute to aberrant T cell proliferations and participate in the persistent immune activation in cGVHD paving the way for novel targeted therapies.

2020-04-12 | E-MTAB-8911 | biostudies-arrayexpress

Somatic mutations in lymphocytes in patients with immune-mediated aplastic anemia

Project description:In this study, we investigated somatic mutations of CD4+ and CD8+ T cells in patients with immune-mediated aplastic anemia (AA). To understand the role of mutations, we performed single-cell level analysis of 6 longitudinal samples of 2 AA patients carrying STAT3 or KRAS and other mutations in CD8+ T cells. The analysis was performed using V(D)J and 5' gene expression platform (10X Genomics). STAT3 mutated clone was clearly distinguishable from other CD8+ T cells and showed a cytotoxic phenotype, attenuated by successful immunosuppressive treatment. Our results suggest that somatic mutations in T cells can alter T cell phenotype warranting further investigation of their role in the pathogenesis of immune-mediated AA.

2021-03-24 | E-MTAB-9969 | biostudies-arrayexpress

Single cell RNA-seq and VDJ-seq of B cells from sheep red blood cells-primed WT and Stch cKO mice

Project description:Once activated, B cells produce the antibodies needed to fight against infection. B cells are necessary for adaptive or specific immunity, which focuses on the destruction of foreign invaders that have gotten past the bodies initial defenses. Heat shock protein family is a group of highly conserved molecular chaperones with important functions in protein folding such as antibody and in signal transduction. Stch (Heat shock 70 kDa protein 13) is a member of the heat shock protein 70 family and is found associated with microsomes. Members of this protein family play a role in the processing of cytosolic and secretory proteins. To explore the role of Stch in B-cell activation and antibody production, we evaluated the transcriptional events and the role of stch pathway on the activation and antibody production of B cells by single cell RNAseq. Splenic lymphocytes were isolated from 7-9-week-old female Stchf/f wildtype (WT) mice and B-cell specific Stch knocked-out (CD19creStchf/f) mice (3 mice/group) using Ficoll (Ficoll-Paque Plus, GE Healthcre). B cells were sorted using B220 microbeads (Cat No. 130-049-501, Miltenyi Biotec, Germany). Their transcriptomes were captured using a 10x chromium system.

2021-03-01 | E-MTAB-8280 | biostudies-arrayexpress

Coupled single-cell RNA, TCR, and barcoded pMHC multimer sequencing, from virus-specific PBMC T-cells

Project description:Virus-specific CD8 T cells from PBMCs of healthy donors and hepatitis patients were enriched for recognition of a panel of feature barcode-labeled pMHC multimers. The phenotypic description was made using gene expression and TCRseq. Samples were pooled and sequenced on the same 10x Genomics sequencing chip and deconvoluted using ADT HashTag antibodies,

2024-05-01 | E-MTAB-13758 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data