Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of Tumor Infiltrating CD8+T Cells Transcriptomes From Control and Manganese(II) Treated C57BL/6 Wild Type Mice

ABSTRACT: Purpose: The goals of this study are to compare the differentially expressed genes of tumor infiltrating CD8+T cells between control and Manganese(II) treated mice. We mainliy fouced on the differentiation of trascription and effector related genes. Methods:C57BL/6 mice were injected subcutaneously in the right flank with B16-F10 and divided into two groups followed by treatment with control (saline) or Manganese(II) respectively. After 14days, mice were euthanized with CO2 and tumor infiltrating CD8+T cells were isolated by FACS. Then RNA of sorted CD8+T cells were generated by deep sequencing using BGISEQ-500. Clean tags were mapped to the mouse genome database (GCF_000001635.25_GRCm38.p5) by HISAT (hierarchical indexing for splicing alignment for transcripts) software. Results: Using an optimized data analysis workflow, we mapped about 60 million sequence reads per sample to the mouse genome (GCF_000001635.25_GRCm38.p5). The significance of the differential expression of genes was defined by the bioinformatics service of Beijing Genomics Institute according to the combination of the absolute value of log2-Ratio ≥ 1 and false discovery rate ≤ 0.001. Conclusions: Manganese(II) enhances the function of tumor infiltrating CD8+T cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE126670 | GEO | 2021/01/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

scRNA and TCR seq of CD8 TILs of WT and Card11 mutant mice(E134G/K215M)

Project description:To investigate the impact of Card11 on TIL differentiation, we isolated TILs from B16-F10 tumors of WT mice, E134G mice, and K215M mice and performed scRNA seq. We also sorted tumor-infiltrating lymphocytes (TILs) from melanoma(B16-F10) of WT mice and conducted scRNA and scTCR sequencing. To further investigate the impact of Card11 on TCR clonal diversity, we sorted CD8 T cells from melanoma WT mice or K215M mice and performed scRNA and scTCR sequencing.

2025-04-23 | GSE292543 | GEO

Expression data from FACS-sorted CD8+BTLA+ vs CD8+BTLA- Human Tumor-infiltrating Lymphocytes in Metastatic Melanoma

Project description:Adoptive T-cell Therapy (ACT) involves using tumor-infiltrating lymphocytes (TIL) isolated from metastatic melanoma and expanding them ex vivo prior to infusion into lympho-depleted patients. This is one of the most promising approaches to treat metastatic melanoma, with the rates of clinical response between 48-50% based on studies done at NCI, M.D. Anderson Cancer Center (Houston, TX), and Sheba Medical Center (Tel Aviv, Israel). In the Phase II ACT Trial at M.D. Anderson Cancer Center , our group has uncovered an association between positive clinical response and the amount of CD8+ tumor-infiltrating lymphocytes expressing B and T Lymphocyte Attenuator (BTLA), a reported inhibitory receptor on T-cells. We used microarrays to detail the differences in the global programme of gene expression between CD8+BTLA+ vs CD8+BTLA- TILs in order to understand the molecular basis of the clinical association. TILs were isolated by enzymatically digest the melanoma tumor fragments obtained from Stage IIIc/IV melanoma patients at M.D. Anderson Cancer Center. The TILs were expanded with high-dose IL-2 for two weeks prior to sorting by FACS (fluoresecence-activated cell sorter) for CD8+BTLA+ and CD8+BTLA- susbets. RNA was extracted from each sorted subsets and hybridized on Affymetrix microarrays

2013-01-03 | E-GEOD-43260 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Tumor Infiltrating CD8+T Cells Transcriptomes From Control and Manganese(II) Treated C57BL/6 Wild Type Mice

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Tumor Infiltrating CD8+T Cells Transcriptomes From Control and Manganese(II) Treated C57BL/6 Wild Type Mice

| PRJNA522908 | ENA

Gene expression profile at single cell level of total tumor-infiltrating CD8+ T cells

Project description:Goblet cells are considered as a homogeneous population in total tumor-infiltrating CD8+ T cells. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of total tumor-infiltrating CD8+ T cells.

2022-08-23 | GSE211690 | GEO

Gene expression profile at single cell level of CD8+ tumor infiltrating lymphocytes from the CT26 murine colon carcinoma model subdivided by antigen binding capacity

Project description:CD8+ tumor infiltrating lymphocytes can have a range of binding strengths for a single tumor associated antigen. The impact this has on the transcriptional profile of the diverse CD8+ tumor infiltrating lymphocyte population was investigated by single cell RNA sequencing.

2022-11-14 | GSE212980 | GEO

Molecular profile of tumor-specific CD8+ T cell hypofunction in cancer

Project description:Comparison of genome-wide mRNA expresson between tumor-infiltrating CD8+ T cells from the tumor (hypofunctional T cells) and periphery (functional T cells) Mechanisms of self-tolerance often result in CD8+ tumor-infiltrating lymphocytes (TIL) with a hypofunctional phenotype incapable of tumor clearance. Using a solid tumor model in mice, we found that CD8+ T cells became tolerized in less than 24 hours in an established tumor environment. To define the collective impact of pathways suppressing TIL function, we compared genome-wide mRNA expression of tumor-specific CD8+ T cells from the tumor and periphery. Notably, gene expression induced during TIL hypofunction more closely resembled self-tolerance than viral-exhaustion. Differential gene expression was refined to identify a core set of genes that defined hypofunctional TIL; these data comprise the first âmolecular profileâ of tumor-specific TIL that are naturally responding and represent a polyclonal repertoire. The molecular profile of TIL was further dissected to determine the extent of overlap and distinction between pathways that collectively restrict T cell functions. As suggested by the molecular profile of TIL, protein expression of inhibitory receptor LAG-3 was differentially regulated throughout prolonged late-G1/early-S phase of the cell cycle. Our data may accelerate efficient identification of combination therapies to boost anti-tumor function of TIL specifically against tumor cells. 4 samples, 3 biological replicates per group.

2016-04-03 | E-GEOD-79858 | biostudies-arrayexpress

Transcriptome analysis of various TOX+ and TOX- tumor-infiltrating CD8 T cells and in vitro TOX over-expressing T cells.

Project description:TOX is selectively expressed in tumor-infiltrating CD8 T cells however the role of TOX in peripheral CD8 T cells is not known. The two goals of this study are to elucidate transcriptional changes between TOX-sufficient and TOX-deficient tumor infiltrating CD8 T cells and to elucidate the molecular program induced by TOX overexpression in peripheral CD8 T cells.

2019-06-24 | GSE126973 | GEO

ATACseq profiling of various TOX+ and TOX- tumor-infiltrating CD8 T cells

Project description:TOX is selectively expressed in tumor-infiltrating CD8 T cells however the role of TOX in peripheral CD8 T cells is not known. The goal of this study is to elucidate changes in chromatin accessibility determined by ATAC-seq between TOX-sufficient and TOX-deficient tumor infiltrating CD8 T cells isolated from murine tumors.

2019-06-24 | GSE126970 | GEO

Expression data from FACS-sorted CD8+BTLA+ vs CD8+BTLA- Human Tumor-infiltrating Lymphocytes in Metastatic Melanoma

2013-01-03 | GSE43260 | GEO

proteome analysis of Lung tissue of mice bearing B16-F10-luc-G5 melanoma tumor with sleep fragmentation and with or with out the asdmistration of GL-pp

Project description:Proteome analysis of Lung tissue of mice bearing B16-F10-luc-G5 melanoma tumor with sleep fragmentation and with or with out the asdmistration of GL-pp. The mice were randomly divided into 4 groups: control group in general condition with no further treatment (CON group), tumor group with the burden of B16-F10-luc-G5 cells (Tumor group), T+SF group with SF and the burden of B16-F10-luc-G5 cells (T+SF group), and GL-pp group with SF, tumor cells burden, and the administration of 80 mg/kg GL-pp (GL-pp group). B16-F10-luc-G5 cells (5 × 1000000 cells/100 µL per mouse) were injected into the mice through the tail vein. The lung tissue of T+SF group and GL-pp group were analyzed by the proteome.

2021-09-10 | PXD025171 | Pride

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