Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Clonal cooperation through soluble metabolite exchange facilitates metastatic outgrowth by modulating Allee effect

ABSTRACT: Clonal cooperation through soluble metabolite exchange facilitates metastatic outgrowth by modulating Allee effect

PROVIDER: PRJNA925850 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23150322_1.fastq.gz	Fastqsanger.gz
	SRR23150322_2.fastq.gz	Fastqsanger.gz
	SRR23150324_1.fastq.gz	Fastqsanger.gz
	SRR23150324_2.fastq.gz	Fastqsanger.gz
	SRR23150326_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 60

Similar Datasets

Clonal cooperation through soluble metabolite exchange facilitates metastatic outgrowth by modulating Allee effect

Project description:Tumours feature substantial heterogeneity of phenotypically distinct lineages. Although intra-clonal interactions between co-existing lineages is emerging as major contributor shaping tumor evolution, the extent and nature of interactions remain largely unknown. Here, we show that Allee effect, i.e., growth dependency on population size, is pervasive, and that intra-clonal soluble metabolite exchange alleviates the Allee thresholds to growth. Additionally, we find clear evidence for cooperative ecological interactions between lineages in that all clones are alleviated by reconditioned medium from the whole population; pairwise combinations of clones typically show cooperative interactions, as do polyclonal combinations. In mouse xenograft models, polyclonal metastasis formed from groups of interacting clones displayed enhanced metastatic outgrowth highlighting the physiological role of metabolic cooperation in vivo. Our results bring forward intra-tumor metabolite exchange as a modulator of tumor ecology and metastasis.

2023-09-01 | GSE223348 | GEO

Regulators of histone exchange

Project description:Regulators of histone exchange

| PRJNA927495 | ENA

Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth

Project description:Axillary bud outgrowth determines plant shoot architecture and is under control of endogenous hormones and a fine-tuned gene expression network. Some genes associated with shoot development are known targets of small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets in axillary buds are unknown. In this study, we employed next-generation sequencing, gene expression analysis and metabolite profiling to identify sRNAs and quantify distinct hormones, respectively, in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.). Differential accumulation of abscisic acid (ABA), gibberellins (GA), and cytokinins indicates a dynamic balance of these hormones during sugarcane bud outgrowth. A number of repeat-associated siRNAs generated from distinct transposable elements and genes were highly expressed in both inactive and developing buds. RT-qPCR results revealed that specific miRNAs were differentially expressed in developing buds and some correlate negatively with the expression of their targets. Expression patterns of miR159 and its experimentally confirmed target GAMYB suggest they play roles in regulating ABA and GA-signaling pathways during bud outgrowth. Our work reveals, for the first time, differences in composition and expression profiles of small RNAs and targets between inactive and developing buds that, together with the endogenous balance of specific hormones, may be important to regulate axillary bud outgrowth in plants. Examination of small RNA populations in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.)

2012-12-31 | E-GEOD-38894 | biostudies-arrayexpress

Water-Soluble Polymer

Project description:Water-Soluble Polymer Raw sequence reads

| PRJNA1039989 | ENA

Transcriptome analysis during axillary shoot outgrowth

Project description:In plant axillary bud dormancy and outgrowth are regulated by phytohormones, but it is still unknown about its molecular mechanism. We reveal that Arabidopsis axillary buds located at axil of rosette leaves show dormancy and that this is broken by the decapitation of main stem, resulting in the bud outgrowth. To investigate about the molecular mechanisms of dormancy and outgrowth, we carried out gene expression analysis during axillary shoot outgrowth in Arabidopsis wild type Columbia accession. Since axillary buds did not initiate outgrowth (dormancy) at 5 day after bolting of main stem, we used 5-day bolted plants as a control (before decapitation). Then, main stems were decapitated, and axillary shoots were collected at 24 hours after decapitation (named as growing shoot). Total RNA was prepared from either control or growing shoots and used for the microarray analysis. We carried out duplicate microarray analysis using independent plant materials.Ref):Tatematsu et al., Plant Physiol. 138: 757-766 (2005). Keywords: Expression profilling by array 4 samples were used in this experiment

2009-11-17 | E-GEOD-18987 | biostudies-arrayexpress

Sediment microbial metabolite

Project description:Sediment microbial metabolite

| PRJNA804568 | ENA

Soluble SORLA enhances neurite outgrowth and regeneration through activation of EGFR and MAPK pathways

Project description:SORLA is a type I transmembrane component associated with Alzheimers disease (AD) risk. Although SORLA is abundantly expressed in neurons, physiological roles for SORLA remain yet unclear. Here, we show that cultured neurons overexpressing SORLA (SORLA TG) feature enhanced neurite length, and accelerated neurite regeneration with wounding. Enhanced accumulation of a soluble SORLA form (sSORLA) is observed in SORLA TG neurons, where purified sSORLA can sufficiently drive neurite extension and regeneration. Phosphoproteomic analysis indicates enrichment of phosphoproteins related to the EGFR/ERK pathway in SORLA TG hippocampus. We find that sSORLA can co-precipitate with EGFR in vitro, where sSORLA treatment can induce EGFR Y1173 phosphorylation in cultured neurons. sSORLA also triggers Erk activation and downstream c-fos upregulation/nuclear translocation, where pharmacological EGFR or ERK inhibition reversed enhancements in sSORLA-dependent neurite regeneration. Together, these results implicate the EGFR as a sSORLA receptor which activates ERK/c-Fos pathways to enhance neurite extension, outgrowth and regeneration.

2020-05-12 | MSV000085400 | MassIVE

Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth

Project description:Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth

| PRJNA853548 | ENA

Transcriptome analysis during axillary shoot outgrowth

Project description:In plant axillary bud dormancy and outgrowth are regulated by phytohoromones, but it is still unknown about its molecular mechanism. We reveal that Arabidopsis axillary buds located at axil of rosette leaves show dormancy and that this is broken by the decapitation of main stem, resulting in the bud outgrowth. To investigate about the molecular mechanisms of dormancy and outgrowth, we carried out gene expression analysis during axillary shoot outgrowth in Arabidopsis wild type Columbia accession. Since axillary buds did not initiate outgrowth (dormancy) at 5 day after bolting of main stem, we used 5-day bolted plants as a control (before decapitation). Then, main stems were decapitated, and axillary shoots were collected at 24 hours after decapitation (named as growing shoot). Total RNA was prepared from either control or growing shoots and used for the microarray analysis. We carried out duplicate microarray analysis using independent plant materials.Ref):Tatematsu et al., Plant Physiol. 138: 757-766 (2005). Keywords: Expression profilling by array

2009-11-18 | GSE18987 | GEO

Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth [bulkRNAseq_AKPS]

Project description:Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth [bulkRNAseq_AKPS]

| PRJNA853559 | ENA