Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome wide analysis of Open Chromatin Regions in memory OT-I cells

ABSTRACT: Genome wide analysis of Open Chromatin Regions in memory OT-I cells

PROVIDER: PRJNA639157 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12005418_1.fastq.gz	Fastqsanger.gz
	SRR12005418_2.fastq.gz	Fastqsanger.gz
	SRR12005419_1.fastq.gz	Fastqsanger.gz
	SRR12005419_2.fastq.gz	Fastqsanger.gz
	SRR12005420_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Genome wide analysis of Open Chromatin Regions in memory OT-I cells

Project description:Cognate antigen signals control CD8+ T cell priming, expansion size and effector versus memory cell fates, however, it is not clear whether they can also modulate the functional features of memory CD8+ T cells. We observed that OT-I cells that were primed with weak cognate antigen signals incorporate more cytokine signals, leading to a hypothesis that CD8+ T cells that receive weak TCR signals require cytokine signals to form functional memory. Using a previously described mouse model in which IL-2 signaling via its high affinity receptor CD25 is selectively impaired, the “Il2ramut/mut” mouse, we conducted a comparative analysis of gene expression and epigenetic landscape of Il2ramut/mut and WT OT-I memory cells that were primed with strong (Lm-Ova N4) versus weak (Lm-Ova T4). RNA seq data showed that both TCR and IL-2 priming signals have minimal effect on gene expression in resting memory CD8 T cells, but they significantly modify the epigenetic landscape of the memory CD8 T cells. These findings have important contributions to the current understanding of how priming signals program memory CD8 T cells in vivo.

2020-09-30 | GSE152392 | GEO

Memory OT-I cells

Project description:Memory OT-I cells

| PRJNA639155 | ENA

Next-generation sequencing of three memory OT-I cell subsets from mice infected with Listeria monocytogenes

Project description:Purpose: RNA-seq analysis of three memory OT-I cell subsets (from a Klrg1-Cre fate reporter mouse model) isolated from the spleen of C57BL/6 mice infected with Listeria monocytogenes. The hypothesis tested in the present study was that KLRG1+ effector CD8 T lymphocytes differentiate into KLRG1- memory CD8 T lymphocytes and provide long-lasting immunity against infectious diseases and malignancies. Methods: Total RNA was obtained from FACS-purified OT-I cell subsets isolated from spleen 104 (experiment 1) and 110 days post infection (experiment 2) with ovalbumin-expressing Listeria monocytogenes (LM-OVA). Results: Using RNA-seq technology, we performed genome-wide transcriptional profiling of three memory OT-I cells (KLRG1+ Reporter+, KLRG1- Reporter+ (exKLRG1) and KLRG1- Reporter-) and identified 36 genes differentially expressed (> 1.5-fold) between exKLRG1 and KLRG1- Reporter- memory OT-I cells, and 132 differentially expressed genes between exKLRG1 and KLRG1+ Reporter+ memory OT-I cells. We then confirmed the expression of 15 genes/molecules by qRT-PCR and/or flow cytometry. Conclusions: Our study represents the first fate mapping analysis of KLRG1+ effector OT-I cells, demonstrates that KLRG1+ effector OT-I cells differentiate into all memory T cell lineages thereby promoting protective immunity. RNA-seq also identified CX3CR1 as a marker of circulating exKLRG1 early memory OT-I cells.

2018-03-01 | GSE110629 | GEO

Next-generation sequencing of three memory OT-I cell subsets from mice infected with vesicular stomatitis virus

Project description:Purpose: RNA-seq analysis of three memory OT-I cell subsets (from a Klrg1-Cre fate reporter mouse model) isolated from the spleen of C57BL/6 mice infected with vesicular stomatitis virus. The hypothesis tested in the present study was that KLRG1+ effector CD8 T lymphocytes differentiate into KLRG1- memory CD8 T lymphocytes and provide long-lasting immunity against infectious diseases and malignancies. Methods: Total RNA was obtained from FACS-purified OT-I cell subsets isolated from spleen 70 days post infection with ovalbumin-expressing vesicular stomatitis virus (VSV-OVA) (experiment 3). Results: Using RNA-seq technology, we performed genome-wide transcriptional profiling of three memory OT-I cells (KLRG1+ Reporter+, KLRG1- Reporter+ (exKLRG1) and KLRG1- Reporter-) and identified 36 genes differentially expressed (> 1.5-fold) between exKLRG1 and KLRG1- Reporter- memory OT-I cells, and 132 differentially expressed genes between exKLRG1 and KLRG1+ Reporter+ memory OT-I cells. We then confirmed the expression of 15 genes/molecules by qRT-PCR and/or flow cytometry. Conclusions: Our study represents the first fate mapping analysis of KLRG1+ effector OT-I cells, demonstrates that KLRG1+ effector OT-I cells differentiate into all memory T cell lineages thereby promoting protective immunity. RNA-seq also identified CX3CR1 as a marker of circulating exKLRG1 early memory OT-I cells.

2018-03-01 | GSE110706 | GEO

Profiling open chromatin regions in human myometrial tissues

Project description:Profiling open chromatin regions in human myometrial tissues

| PRJNA565904 | ENA

Identification of open chromatin regions in mouse cardiopharyngeal mesoderm

Project description:Identification of open chromatin regions in mouse cardiopharyngeal mesoderm

| PRJNA726796 | ENA

RNAseq of memory cocktail versus IL-2 grown OT-I CD8 T cells

Project description:Cytotoxic T cells are typically expanded ex vivo for adoptive immunotherapy by culture with IL-2. This culture period leads to a differentiated phenotype and acquisition of effector function, as well as a loss of in vivo proliferative capability and anti-tumor efficacy. Here, we report antigen-specific and polyclonal expansion of cytotoxic T cells in a cocktail of cytokines and small molecules that leads to a memory-like phenotype in mouse and human cells even during extended culture, leading to enhanced in vivo expansion and tumor control. OT-I CD8 T cells were cultured for 14 days in either IL-2 or a cocktail of memory inducing small molecules and cytokines (IL-7, IL-21, 2-deoxyglucose and TWS119). Populations were sorted, IL-2 cells were CD44+CD62L-, cocktail cells were sorted into CD44+CD62L-, CD44+CD62L+ and CD44lowCD62L+ populations, and naive OT-I cells were CD44-CD62L+. Total RNA was extracted from each population and prepared for sequencing as three technical replicates.

2014-08-12 | E-GEOD-54877 | biostudies-arrayexpress

Transcriptional profiling of OT-1 cells during in vitro memory formation after high- or low-affinity priming

Project description:To understand the impact of TCR affinity during priming on memory formation, we performed transcriptional profiling of OT-1 cells at different time points after stimulation with high- or low-affinity ligands. Our findings indicate that low-affinity stimulaation is associated with earlier memory formation.

2020-01-06 | GSE102189 | GEO

Profiling open chromatin regions in human myometrial tissues

Project description:The open chromatin regions of nonpregnant and term pregnant human myometrial tissues were assessed by ATAC-seq to gain insight on potential genome regulatory elements in vivo. patterns of accessible genome change between NP and TP myometrium, leading to altered enrichment of binding motifs for hormone and muscle regulators such as the progesterone receptor (PGR), Krüppel-like factors and MEF2A transcription factors.

2019-11-28 | GSE137549 | GEO

Redirection of therapeutic T cells to a bone marrow niche improves their persistence and anti-tumor functions: transcription profiling by array of resting memory OT-I T_CXCR4) or OT-I T_Control cells isolated from the spleen 90 days following DC vaccination.

Project description:This study reports the improvement in function and antitumor efficacy of CXCR4 overexpression in therapeutic CD8+ T cells. Polyclonal CD8+ T cells from OT-I C57BL/6 (B6) mice were transduced with a modified pMP71 retroviral vector containing murine Cxcr4 and Gfp reporter sequences (T_CXCR4) or with a control vector containing Gfp alone (T_Control), and co-transferred into to B6 mice that were then vaccinated with peptide-pulsed DC. 90 days following DC vaccination, lymphocytes were isolated from the spleen and resting memory OT-I T_CXCR4 and OT-I T_Control cells were FACS sorted to perform gene expression profiling.

2018-03-28 | E-MTAB-6091 | 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