Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Understanding the Mechanism of Action of the Anti-Dandruff Agent Zinc Pyrithione against Malassezia restricta.

ABSTRACT: Purpose: Understanding the Mechanism of Action of the Anti-Dandruff Agent Zinc Pyrithione against Malassezia restricta. Methods: The transcriptome profile of the ZPT-treated M. restricta cells compared to that of untreated cells were generated by RNA-Seq using Illumina HiSeq. Generated raw reads that passed quality filters were mapped to the reference genome. Mapped reads were counted by featureCounts in Subread package v1.4.3 and the relative transcript abundance was TPM-normalized. Results: A number of genes were differentially expressed in the ZPT-treated cells, which include genes involved in zinc transporter, mitochondirial function, TCA cycle, electron transport chain and lipase.

ORGANISM(S): Malassezia restricta

PROVIDER: GSE112036 | GEO | 2018/12/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq transcriptional profiling of wildtype and Pax5 knockout mouse pro-B cells

Project description:Total RNA was isolated from wild type and Pax5-/- pro-B cells. Samples were sequenced on an Illumina Hiseq 2000 at the Beijing Genomics Institute to produce 90bp paired-end reads. Reads were aligned to the mm10 genome using Subread with unique alignment. The number of read pairs mapped to each gene in the NCBI RefSeq annotation was counted using the featureCounts function of the Rsubread package.

2018-10-07 | GSE99153 | GEO

RNA-seq of the human HCC cell line PLC5 after 72 hours treatment with either MAGEA3 shRNA or Scramble control

Project description:To better understand the mechanism by which MAGEA3 contributes to HCC progression, we conducted RNA sequencing in the PLC5 HCC cell line after 72 hours of treatment with scramble or sh8375 in triplicate. RNA-sequencing was conducted on poly-A enriched RNA, 100 bp single reads using an Illumina HiSeq2500 instrument. Libraries were constructed using the TruSeq RNA Library Prep Kit v2. Raw sequencing reads were mapped to the GRCh38 reference genome (USCS) using STAR (2.4.2g1). Aligned reads were mapped to GRCh38 genetic features using featureCounts from the subRead package with default settings. Data analysis included differential gene expression between conditions and gene set enrichment analysis.

2021-05-19 | E-MTAB-8860 | biostudies-arrayexpress

RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization

Project description:The goal of this study is to perform RNAseq in different sub-types of the zebrafish embryonic dorsal aorta (DA) at 28-30 hpf using TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN, Cat No. 74034). High quality RNA (RIN > 8.0) was sent for RNAseq to the Wellcome Trust Centre for Human Genetics (WTCHG). 2.2 ng of total RNA was used to generate SMARTer libraries for low-input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities, trimmed where 20% of the bases were below quality score 20, and filtered to exclude adapters using Trimmomatic (Version 0.32). Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1). To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads (QC-passed reads count) has been obtain using Samtools mapping statistics (flagstat tool).

2019-06-06 | GSE132259 | GEO

RNA-Seq of ALDH positive and ALDH negative cells from patient-derived xenograft models of colon cancer

Project description:Colon cancer patient-derived xenograft (PDX) models were processed to single cells and sorted by FACS (BD FACS Aria II) for ALDH activity (Aldefluor assay) and DAPI. ALDH Negative and ALDH Positive cells from each PDX model were collected and lysed in RLT buffer and processed for RNA using the RNeasy Mini Plus RNA extraction kit (Qiagen). Samples were processed using Illumina’s TrueSeq RNA protocol and sequenced on an Illumina HiSeq 2500 machine as 2x125nt paired-end reads. Reads were mapped to the human reference genome (assembly hg19) using the STAR aligner (version 2.4.2a). Total read counts per gene were computed using the program “featureCounts” (version 1.4.6-p2) in the “subread” package, with the gene annotation taken from Gencode (version 19).

2021-01-11 | E-MTAB-8927 | biostudies-arrayexpress

RNAseq of LSEC from WT and Bmp9-KO mice in 129/Ola genetic background

Project description:LSEC fom WT and Bmp9-KO 25-weeks female mice were isolated using collagenase and treated for bulk RNAsequencing. The objective was to determine the biological processes that are altered in Bmp9-KO compared to WT, as BMP9 is know to be a vascular quiescence factor produced by hepatic stellate cells. RNAseq reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36 16. The trimmed reads were mapped to the Mus Musculus MM10 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b 17. Unique gene hit counts were calculated by using ‘featureCounts’ from the Subread package v.1.5.2 WT samples are F126, F121, F120, F119, F135 KO samples are F131, F132, F124 and F133

2024-04-30 | E-MTAB-14012 | biostudies-arrayexpress

Malassezia sympodialis

Project description:Malassezia sympodialis Raw sequence reads

| PRJNA509335 | ENA

Metabolic reconstruction of lipid metabolism of Malassezia

Project description:Malassezia species are lipophilic and lipid dependent yeasts belonging to the human and animal microbiota. Typically, they are isolated from regions rich in sebaceous glands. They have been associated with dermatological diseases such as seborrheic dermatitis, tinea versicolor, atopic dermatitis, and folliculitis. Genome sequences of Malassezia globosa, Malassezia sympodialis, and Malassezia pachydermatis lack genes related to fatty acid synthesis. Here, lipid synthesis pathways of M. furfur, M. pachydermatis, M. globosa, M. sympodialis and an atypical variant of M. furfur were reconstructed using genome data and Constraints Based Reconstruction and Analysis. The metabolic reconstruction allowed us to predict variation in the fluxes of each reaction over the network to satisfy the biomass objective function. Proteomic profiling improved and validated the models through data integration. Results suggest that several mechanisms including steroid and butanoate metabolism explain the yeast’s growth under different lipid conditions. Flux differences were observed in production of riboflavin in M. furfur and the biosynthesis of glycerolipids in the atypical variant of M. furfur and Malassezia sympodialis.

2017-10-02 | PXD004523 | Pride

Malassezia

Project description:Malassezia furfur and Malassezia Pachydermatis genome sequencing and assembly

| PRJNA322049 | ENA

Malassezia

Project description:Malassezia furfur and Malassezia Pachydermatis genome sequencing and assembly

| PRJNA288787 | ENA

Malassezia

Project description:Malassezia Genome sequencing

| PRJNA674991 | ENA