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E. coli SymE-SPA binds DNA in a wide variety of genomic locations in vivo [ChIP-seq]

ABSTRACT: E. coli SymE-SPA binds DNA in a wide variety of genomic locations in vivo [ChIP-seq]

PROVIDER: PRJNA771134 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16324020.fastq.gz	Fastqsanger.gz
	SRR16324021.fastq.gz	Fastqsanger.gz
	SRR16324022.fastq.gz	Fastqsanger.gz
	SRR16324023.fastq.gz	Fastqsanger.gz
	SRR16324024.fastq.gz	Fastqsanger.gz

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E. coli SymE-SPA binds DNA in a wide variety of genomic locations in vivo [ChIP-seq]

Project description:The purpose of this experiment was to demonstrate that SymE-SPA binds DNA in vivo when overexpressed, and identify where in the genome SymE-SPA binds. To do this SymE-SPA and an untagged SymE control were expressed, and areas of the genome enriched for SymE-SPA binding were identified.

2021-10-16 | GSE185893 | GEO

ChIP-Seq DnaA-SPA and AcpS-SPA control

Project description:ChIP-seq was performed to map the association of SPA-tagged DnaA across the Escherichia coli MG1655 chromosome during exponential phase growth in LB. As a control to remove background, ChIP-Seq was also performed on SPA-tagged AcpS, a protein that is not known to bind DNA.

2022-10-16 | E-MTAB-12223 | biostudies-arrayexpress

Genomic evidence reveals SPA-regulated developmental and metabolic pathways in dark-grown Arabidopsis seedlings

Project description:Background: Photomorphogenesis is repressed in the dark mainly by an E3 ubiquitin ligase complex comprising CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and four homologous proteins called SUPPRESSOR OF PHYA-105 (SPA1-SPA4) in Arabidopsis. This complex induces the ubiquitination and subsequent degradation of positively acting transcription factors (e.g., HY5, HFR1, PAP1 and others) in the dark to repress photomorphogenesis. Genomic evidence showed a large number of genes regulated by COP1 in the dark, of which many are direct targets of HY5. However, the genomic bases for the constitutive photomorphogenic phenotypes of spaQ remain unknown. Results: Here, we show that >7200 genes are differentially expressed in the spaQ background compared to wild type in the dark. Comparison of the RNAseq data between cop1 and spaQ revealed a large overlapping set of genes regulated by the COP1-SPA complex. In addition, many of the genes coordinately regulated by the COP1-SPA complex are also regulated by HY5 directly and indirectly. Moreover, a large number of genes (~2790) are predominantly regulated by SPA proteins and not by COP1, suggesting that SPA proteins might regulate many biological processes independently of COP1. Conclusions: Taken together, our data reveal that SPA proteins repress photomorphogenesis by controlling expression of a large number of genes in concert with COP1, likely through regulating the abundance of downstream transcription factors in light signaling pathways. Moreover, SPA proteins may function both in a COP1-dependent and –independent manner in regulating many biological processes and developmental pathways in Arabidopsis.

2018-11-05 | GSE112662 | GEO

ChIP-Seq DnaA-SPA and AcpS-SPA control

Project description:ChIP-Seq DnaA-SPA and AcpS-SPA control

| PRJEB56374 | ENA

Comparison of Gene Expression between stromal vascular cells (SVC) and newly identified adipose precursor (SPA)

Project description:We have identified proliferative cells in adipose tissue expressing adipocyte specific genes, which were named small proliferative adipocytes (SPA). Comparison of gene expression by microarray and real time PCR among stromal vascular cells (SVC), SPA and mature adipocyte (MA) revealed that adipocyte specific genes and several neuronal genes were increased in the order of SVC < SPA < MWA. However, proliferin 2 (PLF) was detected only in SPA. We found that SPA changed to lipid laden cells by incubation with differentiation medium containing insulin/dexamethasone/IBMX. In this study, we investigated the gene expression of differentiated SPA (D-SPA) comparing with differentiated SVC (D-SVC). Further study using microarrays and real time PCR revealed that uncoupling protein 1 (UCP1) and PLF were strongly expressed in D-SPA. These data suggested that SPA might be able to differentiate into beige cells.

2018-02-21 | GSE110886 | GEO

Exoproteomes of S. aureus spa type t437 isolates

Project description:A total of 20 S. aureus spa type t437 isolates were used for exoproteome analyses in the present study. Ten of them were selected from MLVA type (MT) 621 group which has was shown to represent the most predominant class of S. aureus isolates with the spa type t437; the other ten isolates belonged to different MTs, namely MT1870, MT4125, MT1035, MT1297, MT2075, MT1875, MT2322, MT1831, MT4183 and MT1830.

2019-05-24 | PXD009082 | Pride

Brachypodium distachyon strain:Spa-Sou-GR6.4 | cultivar:Spa-Sou-GR6.4

Project description:Brachypodium distachyon strain:Spa-Sou-GR6.4 | cultivar:Spa-Sou-GR6.4 Genome sequencing

| PRJNA333770 | ENA

Brachypodium distachyon strain:Spa-Nor-S16D | cultivar:Spa-Nor-S16D

Project description:Brachypodium distachyon strain:Spa-Nor-S16D | cultivar:Spa-Nor-S16D Genome sequencing

| PRJNA333758 | ENA

Brachypodium distachyon strain:Spa-GU5-1 | cultivar:Spa-GU5-1

Project description:Brachypodium distachyon strain:Spa-GU5-1 | cultivar:Spa-GU5-1 Genome sequencing

| PRJNA334987 | ENA

Brachypodium distachyon strain:Spa-Nor-S19A | cultivar:Spa-Nor-S19A

Project description:Brachypodium distachyon strain:Spa-Nor-S19A | cultivar:Spa-Nor-S19A Genome sequencing