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Gene expression analysis of WT and Tfap4–/– OT-I cells activated by Listeria monocytogenes expressing ovalbumin

ABSTRACT: Gene expression of Tfap4–/– and WT OT-I T cells were compared 4 or 6 days after activation with Listeria monocytogenes infection in vivo with the ERCC spike-in RNA control.

ORGANISM(S): Mus musculus

PROVIDER: GSE58076 | GEO | 2014/07/13

SECONDARY ACCESSION(S): PRJNA248826

REPOSITORIES: GEO

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Gene expression analysis of WT and Tfap4–/– OT-I cells activated by Listeria monocytogenes expressing ovalbumin

Project description:Gene expression of Tfap4–/– and WT OT-I T cells were compared 4 or 6 days after activation with Listeria monocytogenes infection in vivo with the ERCC spike-in RNA control. Naive CD8+ T cells from Tfap4–/– OT-I or control WT OT-I TCR transgenice mice were adoptively transferred to congenic host mice that were subsequently infected with Listeria monocytogenes expression ovalbumin. Activated OT-I cells were harvested 4 days or 6 days after infection and gene expression was compared using microarray. 1 μL of 1:1,000 diluted External RNA Controls Consortium (ERCC) RNA Spike-In Control Mixes (Ambion) was added to total RNA extracted from 1 x 10^5 cells prior to amplification. Gene expression was quantitated by RMA normalization to Signal intensity and signal intensities were further converted by formula obtained from linear regression of signals for spiked-in control RNA between samples to obtain cell number-normalized gene expression.

2014-07-13 | E-GEOD-58076 | biostudies-arrayexpress

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

ATAC-seq of naive and three effector OT-I cell subsets from mice infected with Listeria monocytogenes

Project description:Purpose: ATAC-seq analysis of naive and three effector OT-I cell subsets (from a Klrg1-Cre fate reporter mouse model) isolated from the spleen of C57BL/6 mice 0 and 8 days post infection with OVA-expressing Listeria monocytogenes. The hypothesis tested in the present study was that chromatin remodeling in KLRG1+ effector CD8 T lymphocytes promotes the differentiation into KLRG1- memory CD8 T lymphocytes that provide long-lasting immunity against infectious diseases and malignancies. Methods: DNA was obtained from 50,000 FACS-purified OT-I cell subsets isolated from spleen 0 and 8 days post infection with ovalbumin-expressing Listeria monocytogenes (LM-OVA) (experiment 3). Results: Using ATAC-seq technology, we analyzed the chromatin accessibility landscape of naive and three effector OT-I cells (KLRG1+ Reporter+, KLRG1- Reporter+ (exKLRG1) and KLRG1- Reporter-). 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 identified CX3CR1 as a marker of circulating exKLRG1 early memory OT-I cells, and ATAC-seq analysis revealed that chromatin remodeling enabled exKLRG1 memory cells to exhibit both a high cytotoxic and proliferative capacity.

2018-03-01 | GSE110876 | GEO

Microarray analysis of WT and Tfap4-KO CD8 T cells during early activation

Project description:Gene expression of Tfap4–/– and WT CD8+ T cells were compared after activation with anti-CD3 and anti-CD28 antibodies in vitro or with Listeria monocytogenes infection in vivo

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Listeria monocytogenes transcriptional response to bile

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Project description:The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator HrcA, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DhrcA stationary phase cells were compared to wt to identify hrcA-dependent genes. We identified 61 HrcA-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression between ΔhrcA and wt. Combined with microarray analysis, Hidden Markov Model searches show HrcA directly repress at least 8 genes. Keywords: Listeria monocytogenes, HrcA regulon, stationary phase

2007-11-03 | GSE7517 | GEO

CtsR Regulon in Listeria monocytogenes

Project description:The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator CtsR, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DctsR log phase cells were compared to both wt and ictsR-mcsA log phase cells grown with 0.5mM IPTG to identify CtsR-dependent genes.We identified 62 CtsR-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression either between ΔctsR and wt or between ΔctsR and ictsR-mcsA. Keywords: Listeria monocytogenes, CtsR regulon, log phase

2007-10-14 | GSE7514 | GEO

Listeria monocytogenes exposure to chlorine dioxide

Project description:Listeria monocytogenes strain 10403S has been studied extensively for stress response activity toward multiple stressors (acid, osmotic, cold, high temperature, etc.) as well as multiple stress regulons (SigB, CtsR, HrcA, etc.). Here we aimed to determine the transcriptional response of Listeria monocytogenes in early log phase towards the strong oxidative stress imposed by ClO2. The elucidation of such a response allows for further a more completel understanding of the mechanism of inactivation by sanitizers, specifically ClO2.

2014-03-07 | GSE48187 | GEO

Gene expression profile in peritoneal macrophage infected with Listeria monocytogenes

Project description:Several Toll-like receptors are activated by Listeria monocytogenes infection, resulting in the activation of MyD88 dependent signaling pathway. However, the negative role of MyD88 in gene expresson is unclear. To address this, we performed microarray analysis of mRNAs from WT or MyD88-/- peritoneal macrophages infected with Listeria monocytogenes.

2014-06-29 | GSE52115 | GEO

Surface Proteins of Listeria monocytogenes

Project description:Listeria monocytogenes cells (strain LI0521) were digested with trypsin for the identification of surface proteins. The supernatant was filter-sterilized and subjected to identification by LC-MS/MS. Concurrently secreted or shed proteins were identified by isolating filter-sterilized supernatants following incubation of L. monocytogenes cells in buffer without trypsin. This was followed by trypsin digest of the sterilized supernatant and identification by LC-MS/MS.

2013-08-27 | PXD000035 | Pride

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