Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of epigenetic recovery factor from medicinal-herb (Descurainia sophia) treated asthma based on multi-omics approach [RNA-Seq]

ABSTRACT: Expression profiles of Saline, OVA, and Herb treated mice samples. RNA extracted with the Purelink RNA kit was used for cDNA library preparation with the TruSeq Library Prep Kit (Illumina) and sequenced on the NextSeq500.

ORGANISM(S): Mus musculus

PROVIDER: GSE114586 | GEO | 2018/12/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identification of epigenetic recovery factor from medicinal-herb seeds (Descurainia sophia) treated asthma based on multi-omics approach

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-12-26 | GSE114587 | GEO

Identification of epigenetic recovery factor from medicinal-herb (Descurainia sophia) treated asthma based on multi-omics approach [Methyl-Seq]

Project description:Sequencing of bisulfite-converted mouse genomic DNA captured on SureSelect Methyl-Seq

2018-12-26 | GSE114512 | GEO

Identification of epigenetic recovery factor from medicinal-herb seeds (Descurainia sophia) treated asthma based on multi-omics approach

Project description:Identification of epigenetic recovery factor from medicinal-herb seeds (Descurainia sophia) treated asthma based on multi-omics approach

| PRJNA471850 | ENA

Identification of epigenetic recovery factor from medicinal-herb (Descurainia sophia) treated asthma based on multi-omics approach [Methyl-Seq]

Project description:Identification of epigenetic recovery factor from medicinal-herb (Descurainia sophia) treated asthma based on multi-omics approach [Methyl-Seq]

| PRJNA471639 | ENA

Identification of epigenetic recovery factor from medicinal-herb (Descurainia sophia) treated asthma based on multi-omics approach [RNA-Seq]

Project description:Identification of epigenetic recovery factor from medicinal-herb (Descurainia sophia) treated asthma based on multi-omics approach [RNA-Seq]

| PRJNA471859 | ENA

Discovery and mechanistic studies of cytotoxic cyclotides from the medicinal herb Hybanthus enneaspermus (Linn) F. Muell

Project description:Cyclotides are a family of plant-derived peptides characterized by a ~30 amino acid cyclic backbone and a cystine knot motif. Cyclotides have diverse bioactivities, and in particular their cytotoxicity has attracted significant attention for its potential anti-cancer applications. Hybanthus enneaspermus is a medicinal herb widely used in India as a natural libido enhancer, and a previous study indicated that it may contain cyclotides. In the current study, 11 novel cyclotides and one known cyclotide (cycloviolacin O2) were identified and isolated from H. enneaspermus. Their sequences were determined using tandem MS, and NMR analysis of six of these cyclotides indicates their three-dimensional structures are similar to those of other known cyclotides. The most abundant cyclotide in this plant, hyen D, has comparable cytotoxicity against cancer cells to cycloviolacin O2, the most cytotoxic cyclotide discovered so far. Herein we provide a mechanistic insight into the mode-of-action of the novel cyclotides’ cytotoxicity. Hyen D, E, L, M, and cycloviolacin O2 preferentially interacted with model lipid membranes containing phospholipids with phosphatidylethanolamine-headgroups, as measured by surface plasmon resonance. Cyclotide-membrane interactions correlated with cytotoxicity, suggesting that membrane binding underpins cytotoxicity. Overall, this study helps broaden knowledge on the indigenous Indian herb H. enneaspermus, and reports the discovery of novel cyclotides with potent anti-cancer activity.

2020-05-13 | PXD017924 | Pride

REVERSIR platform for the tailored control of GalNAc-siRNA conjugate pharmacology

Project description:Primary mouse hepatocytes were treated with 1 nM TTR-siRNA and 10 nM scrambled or TTR-REVERSIR by in vitro free uptake for 24 h. RNA extracted with the Purelink RNA kit (ThermoFisher) was used for cDNA library preparation with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on the NextSeq500 desktop sequencer (Illumina), all according to manufacturers’ instructions. Raw RNA-seq reads were filtered with minimal mean quality scores of 25 and minimal remaining length of 36, using fastq-mcf. Filtered reads were aligned to the Mus musculus genome (NCBIM37) using STAR with default parameters. Uniquely aligned reads were counted by featureCounts. Differential gene expression (DEG) analysis was performed by the R package DESeq2. Here, we report the rapid and potent reversal of GalNAc-siRNA-mediated RNAi activity in vivo with REVERSIR technology, which is based on short, synthetic high-affinity oligonucleotide complementary to the siRNA guide strand. The modular, sequence-specific nature of the REVERSIR platform has the potential to enhance the therapeutic profile of any long-acting GalNAc-siRNA conjugate to enable fine-tuned control of RNAi pharmacology

2018-05-02 | GSE110620 | GEO

RNA-Seq in HEK293T human cells

Project description:RNA-Seq procedure was used for analysis of expression in HEK293T cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 10 millions of reads were generated for each sample.

2019-12-03 | GSE130262 | GEO

Heat-shock influence on gene expression in HEK293T human cells.

Project description:RNA-Seq procedure was used for analysis of expression in HEK293T cells. Heat shock treatments was performed for 20 min at 43°C. Then heat shock treated cells were incubated for 6 h at 37°C and replicates were separately lysed with Trisol reagent. Total RNA was extracted from cell lysed with Trisol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA Quality was checked with BioAnalyser and RNA 6000 Nano Kit(Agilent). Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length.

2019-12-03 | GSE130493 | GEO

Quantitative analysis of proteome dynamics in a long-term asthma mouse model

Project description:Asthma bronchiale is an inflammatory disease of the respiratory airways and a major factor of increasing health care costs worldwide. The molecular actors leading to asthma are not fully understood and require further investigation. The aim of this study was to monitor the proteome during asthma development from early inflammatory to late fibrotic stages. A time-course-based ovalbumin (OVA) mouse model was applied to establish an asthma phenotype and the lung proteome was analysed at four time points during asthma development (0 weeks = control, 5 weeks, 8 weeks and 12 weeks of OVA treatment).

2021-02-11 | PXD011159 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data