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SCBI Wild type and mutant Expression data

ABSTRACT: Purpose: To compare RNASeq data of wild type and mutants under standard growth conditions (Stationary Phase)28C for 18 h. The mutants were found defective in genes encoding the following proteins: an alkaline metalloprotease secretion protein AprE, GidA, and a PIN domain protein. RNA-seq analysis provided insight into how inactivation of AprE, GidA and a PIN-domain protein influences global gene expression mRNA profiles of wild type and mutants were generated by deep sequencing and mapped to SCBI genome by CLC Gemonic Workstation. The transcriptome profiles of the mutants were compared to the wild type.

ORGANISM(S): Serratia sp. SCBI

SUBMITTER: Louis Tisa

PROVIDER: E-GEOD-60476 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Molecular characterization of protease activity in Serratia sp. strain SCBI and its importance in cytotoxicity and virulence.

Petersen Lauren M LM Tisa Louis S LS

Journal of bacteriology 20140902 22

A newly recognized Serratia species, termed South African Caenorhabditis briggsae isolate (SCBI), is both a mutualist of the nematode Caenorhabditis briggsae KT0001 and a pathogen of lepidopteran insects. Serratia sp. strain SCBI displays high proteolytic activity, and because secreted proteases are known virulence factors for many pathogens, the purpose of this study was to identify genes essential for extracellular protease activity in Serratia sp. strain SCBI and to determine what role protea ...[more]

PMID: 25182493

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SCBI Wild type and mutant Expression data

Project description:Purpose: To compare RNASeq data of wild type and mutants under standard growth conditions (Stationary Phase)28C for 18 h. The mutants were found defective in genes encoding the following proteins: an alkaline metalloprotease secretion protein AprE, GidA, and a PIN domain protein. RNA-seq analysis provided insight into how inactivation of AprE, GidA and a PIN-domain protein influences global gene expression

2014-10-20 | GSE60476 | GEO

Analysis of genes regulated by AS1 and AS2

Project description:AS1 and AS2 encode MYB related protein and AS2-domain containing protein, respectively and may regulate transcription. These genes are involved in the determination of axes of leaves of Arabidopsis thaliana. To know the gene regulation in the leaf development, expression profile among wild-type, as1 and as2 mutants and AS2 overexpression plants were compaired.

2013-03-01 | GSE44028 | GEO

Transcriptome analysis in transgenerational epigenetic inheritance

Project description:The study was performed towards understanding transgenerational epigenetic inheritance at transcriptome level. The founder males of F0 generation (actin-GAL4/Pin; UASRNAi-mts/+), and the resulting, male-line derived F1 (Pin/+; +/+), and F2 (+/+; +/+) generation individuals were used as test lineage, and the wild-type w1118 progeny as control lineage flies. The fly strains used for generating founder F0 line included Pin/CyO-dYFP; UASRNAi-mts/MKRS, actin-GAL4/CyO; +/+, and w1118. Precursor strains, as appropriate, were outcrossed with w1118 to minimize genetic background differences.

2024-01-05 | GSE222543 | GEO

ChIP-seq analysis of GLABRA2 transcription factor DNA-binding sites in wild-type and mutant Arabidopsis seedlings

Project description:GLABRA2 (GL2) is a class IV homeodomain leucine-zipper (HD-Zip IV) transcription factor that is critical for the differentiation of the epidermis in the plant model Arabidopsis. HD-Zip IV transcription factors are characterized by the presence of a lipid sensing domain known as START (for STeroidogenic Acute Regulatory (StAR)-related lipid Transfer). Genome-wide ChIP-seq assays were performed with seedlings expressing EYFP-tagged GL2 wild-type and mutant proteins to test whether the START domain is dispensible for DNA binding in vivo. These experiments included three START domain mutants (gl2_∆ST (listed here as gl2_dSTART), gl2_Amo, and gl2_E375G;R392M) as well as a mutant deleted for the six terminal amino acids of the HD and the entire leucine zipper (gl2_∆HD6;∆ZLZ (listed here as gl2_dZip)). Data analysis revealed DNA binding proficiency for wild-type GL2 and for all three START domain mutants whereas little or no binding was detected for gl2∆HD6;∆ZLZ and the gl2-5 null mutant control. Genomic distributions of the binding sites were similar for wild-type GL2 and the START domain mutants. Most of the ChIP-seq hits were mapped to promoter or intergenic regions, consistent with the role of GL2 as a transcriptional regulator. The relative positions of the binding sites to the transcription start sites were also similar. Gene ontology (GO) classification revealed overlapping functional classes of target genes bound by wild-type GL2 and the START domain mutants.

2022-12-07 | GSE186860 | GEO

Analysis of genes regulated by AS1 and AS2

2013-03-01 | E-GEOD-44028 | biostudies-arrayexpress

MRG15 interactome upon UV irradiation

Project description:The aim of this analysis is to identify the difference between interaction partners of MRG15 wild type and Chromodomain and MRG domain mutants upon UV irradiation. Therefore, MRG15 wild type and mutants (N-terminal FLAG tag) were overexpressed in U2OS cells. After UV irradiation, immunoprecipitation of the constructs was performed using FLAG M2 affinity gel. The constructs were eluted from the beads with 3xFLAG peptide.

2023-07-03 | PXD043089 | Pride

DHHC7-mediated palmitoylation of barttin is a risk factor for Bartter syndrome

Project description:Chloride permeability in the thin and thick ascending limbs of the loop of Henle is a crucial component for urine concentration, with ClC-K/barttin chloride channels as a central component in establishing the cortico-medullary osmotic gradient. Barttin is an accessory subunit of human ClC-K channels, promoting trafficking of the ClC-K/barttin complex to the plasma membrane, increasing channel stability, and switching ClC-K/barttin channels into an active state. Barttin undergoes post-translational palmitoylation, which is essential for channel activation. Here, we identified DHHC7 as a major barttin palmitoyl-acyltransferase, the depletion of which reduced barttin palmitoylation and the macroscopic current amplitudes in cells expressing ClC-K/barttin channels. To investigate a functional role of barttin palmitoylation in vivo, we established Zdhhc7-/- mice. Although barttin palmitoylation was significantly decreased in the kidneys of Zdhhc7-/- animals, it did not result in any pathological consequences for kidney structure or function under physiological conditions. However, when Zdhhc7-/- animals were fed a low-salt diet, they developed hyponatremia and mild metabolic alkalosis, symptoms characteristic of human Bartter syndrome (BS) Type IV with mild progression. Notably, decreased barttin palmitoylation was also found for the R8L barttin mutant identified in human BS Type IV. These data suggest that barttin palmitoylation plays an important role in chloride channel dysfunction in certain variants of BS. Thus, our study provides evidence of the downregulation of barttin palmitoylation as a possible mechanism in the etiology of BS, making the restoration of barttin palmitoylation a promising clinical strategy for the treatment of Type IV BS.

2020-03-31 | PXD017231 | Pride

AKT_Prostate_RAD001_v_PLACEBO

Project description:Transgenic (Probasin driven Myr-AKT)or wild-type littermates were treated with RAD001 or placebo and sacrificed at 12 and 48 hours following the beginning of treatment Keywords = AKT Prostate RAD001 mTOR PIN Keywords: time-course

2004-05-17 | GSE1413 | GEO

The ER Lumenal Hsp70 Protein FpLhs1 Is Important for Conidiation and Plant Infection in Fusarium pseudograminearum

Project description:Secretory proteome of the wild type and FpLhs1 mutants of Fusarium pseudograminearum

2019-05-14 | PXD013850 |

Microarray analysis of PIN lesions from APT121 mouse prostate

Project description:High grade prostate intraepithelial neoplasia (HGPIN) is a precursor lesion for prostate cancer. The APT121 mouse is a model of early stage prostate cancer that develops PIN lesions that progress to adenocarcinoma over a period of 6 months. At 12 wks of age APT121 mouse prostate contains mostly high grade PIN lesions. We compared the transcript profile of RNA from the anterior prostate of age- and genetic background matched wild type and APT121 mice using Affymetric microarrays.

2016-09-09 | GSE50662 | GEO

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