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Arabidopsis isolate:TPS

ABSTRACT: Arabidopsis isolate:TPS Genome sequencing

PROVIDER: PRJNA391706 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5753204.fastq.gz	Fastqsanger.gz
	SRR5753205.fastq.gz	Fastqsanger.gz
	SRR5753206.fastq.gz	Fastqsanger.gz
	SRR5753207.fastq.gz	Fastqsanger.gz

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Single-cell RNA sequencing analysis of mouse totipotent potential stem cells, extended pluripotent stem cells, embryonic stem cells, E17.5 TPS-derived chimeric placental cells, TPS-derived teratomas and TPS-derived blastoids

Project description:It is challenging to derive totipotent stem cells in vitro that functionally and molecularly resemble cells from totipotent embryos. Here, we report that a chemical cocktail enables the derivation of totipotent-like stem cells, designated as totipotent potential stem (TPS) cells, from 2-cell mouse embryos and extended pluripotent stem cells that can be stably maintained long-term in vitro. TPS cells shared features with 2-cell mouse embryos in terms of totipotency markers, transcriptome, chromatin accessibility and DNA methylation patterns. In vivo chimeric assays show that these cells have embryonic and extraembryonic developmental potentials at the single cell level. Moreover, TPS cells can be induced into blastocyst-like structures resembling preimplantation mouse blastocysts. Mechanistically, inhibition of HDAC1/2 and DOT1L activity and activation of RARγ signaling are important for inducing and maintaining totipotent features of TPS cells. Our study opens up a path toward fully capturing totipotent stem cells in vitro.

2022-05-04 | GSE201747 | GEO

Aeromonas hydrophila strain:TPS-30

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RNA seq of Arabidopsis Class II TPS mutants compared to wt, in ZT4, ED (end of day), EN (end of night) and ExtN (extended night)

Project description:The aim was to study the physiological functions of Class II TPS proteins in Tre6P and sugar signaling. For that - T-DNA insertion knockout mutants were identified for all class II TPS genes, then a combinatorial mutants were generated: and tps567 (clade I) knockout and tps891011 (clade II) knockouts were compared to WT.

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RNA-seq analysis of D-tagatose-treated Arabidopsis thaliana inoculated with Hyaloperonospora arabidopsidis isolate Noco-2

Project description:Rare sugars are monosaccharides that are rarely present in nature. To reveal a effect of D-tagatose in plant and the responses to the D-Tagatose in Arabidopsis inoculated with Hyaloperonospora arabidopsidis (Hpa) isolate Noco-2 at gene expression level, we performed a RNA-seq analysis using the Illumina NGS. As a result, there are no significant differences on the gene expression patterns between in mock- and D-tagatose-treated Arabidopsis plants and Hyaloperonospora arabidopsidis.

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Project description:Single-cell RNA sequencing analysis of mouse totipotent potential stem cells, extended pluripotent stem cells, embryonic stem cells, E17.5 TPS-derived chimeric placental cells, TPS-derived teratomas and TPS-derived blastoids

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RNA-seq of HIV-1 infected long-term non-progressors(LTNPs) and typical progressors(TPs)

Project description:HIV-infected long-term non-progressors (LTNPs) are a special group of people who can naturally control HIV and maintain good host immunity. Their mechanism is related to viruses, host genetic characteristics, immune response and other factors, but the relationship between the activation level of innate immunity and long-term non-progression is not clear. Therefore,we hypothesize that LTNPs may have some founction to control the HIV replication in vivo.In this study, we used RNA-seq to investigate the transcription（lncRNA, miRNA and mRNA) profiles of LTNPs and typical progressors (TPs).This study is showing expression spectrum of mRNA and non-coding RNA between HIV-infected long-term non-progressors and typical progressors, and analyze the role of mRNA,IncRNA and miRNA in the HIV infected long-term non-progression based on whole transcriptome level.This study reveals the mechanism of different disease progression between LTNPs and TPs through functional enrichment analysis and differentially expressed genes(DEGs) analysis.

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Project description:Arabidopsis halleri isolate:Lan5 Genome sequencing Haplotype 2

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Effect of overexpression of oilseed rapetrehalose-6-phosphate synthesis gene BnaC02.TPS8 in Arabidopsis

Project description:Trehalose-6-phosphate (T6P) serves as a pivotal signaling molecule, sensing sucrose availability and carbon metabolism. However, the mechanisms governing the regulation of T6P synthase (TPS) genes responsible for anthocyanin accumulation under conditions of low N and high sucrose remain elusive. In a previous study, we demonstrated the positive impact of a cytoplasm-localized class II TPS protein ‘BnaC02.TPS8’ on photosynthesis and seed yield improvement in Brassica napus. Ectopic overexpression of BnaC02.TPS8 in Arabidopsis seedlings resulted in elevated shoot T6P levels under N-sufficient conditions, as well as an increased carbon-to-nitrogen (C/N) ratio, sucrose accumulation, and starch storage under low N conditions. Overexpression of BnaC02.TPS8 in Arabidopsis heightened sensitivity to low N stress and high sucrose levels, accompanied by increased anthocyanin accumulation and upregulation of genes involved in flavonoid biosynthesis and regulation.

2024-11-30 | GSE249127 | GEO

Arabidopsis thaliana isolate:Arabidopsis wild-type Col-0 mutants

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Expression profiling during arabidopsis/downy mildew interaction reveals a highly-expressed effector that attenuates responses to salicylic acid.

Project description:Plants have evolved strong innate immunity mechanisms, but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell. Hyaloperonospora arabidopsidis (Hpa) causes downy mildew on Arabidopsis thaliana, and a genome sequence is available for isolate Emoy2. Here, we exploit the availability of genome sequences for Hpa and Arabidopsis to measure gene-expression changes in both Hpa and Arabidopsis simultaneously during infection. Using a high-throughput cDNA tag sequencing method, we reveal expression patterns of Hpa predicted effectors and Arabidopsis genes in compatible and incompatible interactions, and promoter elements associated with Hpa genes expressed during infection. By resequencing Hpa isolate Waco9, we found it evades Arabidopsis resistance gene RPP1 through deletion of the cognate recognized effector ATR1. Arabidopsis salicylic acid (SA)-responsive genes including PR1 were activated not only at early time points in the incompatible interaction but also at late time points in the compatible interaction. By histochemical analysis, we found that Hpa suppresses SA-inducible PR1 expression, specifically in the haustoriated cells into which host-translocated effectors are delivered, but not in non-haustoriated adjacent cells. Finally, we found a highly-expressed Hpa effector candidate that suppresses responsiveness to SA. As this approach can be easily applied to host-pathogen interactions for which both host and pathogen genome sequences are available, this work opens the door towards transcriptome studies in infection biology that should help unravel pathogen infection strategies and the mechanisms by which host defense responses are overcome.

2014-11-21 | GSE53641 | GEO

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