Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRNA sequencing in raw and processed human breast milk

ABSTRACT: We report the application of miRNA next generation sequencing (NGS) for the analysis of impact of processing on miRNA in human breast milk, donated by 3 volunteers. MiRNA content of total and exosomal fraction was compared between unprocessed milk and sample subjected to either Holder (thermal) pasteurization (HoP) or elevated pressure processing (HPP). NGS reads were mapped to miRBase in order to obtain miRNA counts. Then, we analyzed differences in the miRNA abundance and function between raw and processed material. It was observed that both processing methods reduce number of miRNA reads and HoP is significantly more detrimental to miRNA than HPP.

ORGANISM(S): Homo sapiens

PROVIDER: GSE142282 | GEO | 2019/12/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Next Generation Sequencing (NGS) of miRNAs in human hippocampal tissues

Project description:We carried out Next Generation Sequencing (NGS) to reveal miRNA expression profiles of 16 patients with mTLE+HS and 8 post mortem controls (with median coverage of 10.8 million of unprocessed reads per sample). The sequencing platform identified 1962 miRNA species, out of which 422 miRNAs were present with the coverage of more than 500 reads altogether in all samples. We discovered 9 miRNAs potentially related to mTLE+HS that have not yet been associated with epilepsy.

2017-11-30 | GSE99455 | GEO

Effects of non-thermal methods (High-Pressure Processing, UV-C irradiation and thermoultrasonication) on donor human milk safety and functionality

Project description:This study was conducted in order to evaluate the effects of high-pressure processing, UV-C irradiation and thermo-ultrasonication on donor human milk safety and quality. The results of these methods were then compared with holder pasteurization, which is the current recommended treatment for donor human milk.

2022-03-11 | PXD031216 | Pride

Comparison of mitochondrial unprocessed RNA frequency in wild type and mutant mitochondrial RNA polymerase overexpression flies.

Project description:The goal of this study is to compare the frequency of unprocessed preRNAs in mitochondria. Total mitochondrial RNA profiles of adult flies were generated in triplicates. We analyzed over 100 million reads for each group and used featureCounts to perform quantification allowing a read to be assigned to more than one gene. Using this analysis pipe line, we mapped about 30 million reads per sample to the Drosophila mitochondrial genome and identified a fequency of unprocessed preRNAs as 0.43% in PolrMT group, which is similar to that in PolrMT-E423P flies. These result revealed that overexpression of PolrMT-E423P does not contribute to pre-RNA processing.

2021-12-23 | GSE192549 | GEO

MiRNA sequencing in raw and processed human breast milk

Project description:MiRNA sequencing in raw and processed human breast milk

| PRJNA596469 | ENA

A direct interplay between the co-chaperones Hop and p23 regulates cycle progression and client folding in the Hsp70/Hsp90 chaperone machineries

Project description:Folding of stringent clients requires transfer from Hsp70 to Hsp90. The co-chaperone Hop physically connects the chaperone machineries. Here we define its role from the remodeling of Hsp70/40-client complexes to the mechanism of client transfer and the conformational switching from stalled to active client-processing states of Hsp90. We show that Hsp70 together with Hsp40 completely unfolds a stringent client, the glucocorticoid receptor ligand binding domain (GR-LBD) in large assemblies. Hop remodels these for efficient transfer onto Hsp90. As p23 enters, Hsp70 leaves the complex via switching between binding sites in Hop. To proceed to client folding, current concepts assume that Hop dissociates and the co-chaperone p23 stabilizes the Hsp90 closed state. In contrast, we show that p23 directly interacts with Hop, relieves the stalling Hsp90-Hop interaction and closes Hsp90. This reaction allows folding of the client and is thus the key regulatory step for the progression of the chaperone cycle. To study the interaction between the different proteins, especially p23 and the DP2 domain of Hop, we performed crosslinking-MS.

2022-02-24 | PXD027413 | Pride

MicroRNA expression profiles of bovine milk exosomes in response to Staphylococcus aureus infection

Project description:Milk is an essential source of nutrients to all mammalian offspring, and is rich in a wide variety of immunological components. Recently reported miRNAs that are present in breast milk and are selectively packaged into the exosomes, a type of membrane vesicles, secreted by most cell types. These exosomal miRNAs could be actively delivered into recipient cells, and play a key role in the regulation of innate and adaptive immunity. In the present study we analyzed the lactation-related miRNA expression profiles in bovine milk exosomes at 2 days post-infection with Staphylococcus aureus (S. aureus) using a deep sequencing. Analyzing over 76.44 million sequencing reads, a total of 720 miRNAs including 303 high-confident miRNA candidates were identified by two different approaches. The top 10 highly expressed miRNAs accounted for approximately 80% of all aligned reads, with the remaining miRNAs showing much lower expression. Bta-miR-101, -142-5p, -183, -2285g-3p, -223 and -99a-5p were significantly differentially regulated in S. aureus infected milk compared to their uninfected controls. Target prediction of the differently expressed miRNAs revealed 219 potential target candidates, and 22 unique target genes identified by David Gene Ontology analysis were significantly related to host immune processes and inflammation. This new knowledge of milk miRNA expression in response to S. aureus infection significantly provides new and comprehensive information on milk miRNA composition in general as well as changes occurring during an infection.

2016-10-31 | GSE55144 | GEO

Changes in microRNAs during storage and processing of breast milk of Korean mothers

Project description:Human breast milk (HBM) is the ideal source of nutrients for infants and is rich in microRNA (miRNA). In recent years, expressed breast milk feeding rather than direct breastfeeding is becoming increasingly prevalent for various reasons. HBM requires storage and processing, which can cause various changes in the ingredients. We investigated how the miRNAs in HBM change due to processes often used in real life. HBM samples collected from 10 participants were each divided into 7 groups according to the storage temperature, thawing method, and storage period. And we analyzed the miRNA changes in each group. Significant changes in expression of several miRNAs were confirmed when HBM were heated by microwave immediately after collection, stored at room temperature for 1 week, or frozen for 1 week. Changes in expression were also dependent on the frozen period or thawing method. However, there was no change in the miRNA expression in all samples refrigerated for 1 week. The expression of miRNA can change depending on the diverse processing, storage, and thawing methods of breast milk, and refrigerated storage may be an ideal method to maintain a state of miRNA.

2022-11-03 | GSE216940 | GEO

Penicillium #12 with Ecoli or P. psychrophila and processed with BLANKA

Project description:Penicillium solitum grown on cheese curd agar with either E. coli and Pseudomonas psychrophila and extracted with acn. Data files processed with blank removal algorithm called BLANKA and compared to unprocessed files.

2019-03-14 | MSV000083571 | MassIVE

Evaluation of sample preparation methods for NMR-based metabolomics of cow milk

Project description:The quality of milk metabolome analyzed by nuclear magnetic resonance (NMR) is greatly influenced by the way samples are prepared. Although this analytical method is increasingly used to study milk metabolites, a thorough examination of available sample preparation protocols for milk has not been reported yet. We evaluated the performance of eight milk preparation methods namely (1) raw milk without any processing; (2) skimmed milk; (3) ultrafiltered milk; (4) skimming followed by ultrafiltration; (5) ultracentrifuged milk; (6) methanol; (7) dichloromethane; and (8) methanol/dichloromethane, in terms of spectra quality, repeatability, signal-to-noise ratio, extraction efficiency and yield criteria. A pooled sample of milk was used for all protocols. Skimming, ultracentrifugation and unprocessed milk protocols showed poor NMR spectra quality. Protocols involving multiple steps, namely methanol/dichloromethane extraction, and skimming followed by ultrafiltration produced inadequate results for signal-to-noise ratio parameter. Methanol and skimming associated to ultrafiltration provided good repeatability results compared to the other protocols. Chemical-based sample preparation protocols, particularly methanol, showed more efficient metabolite extraction compared to physical preparation methods. When considering all evaluation parameters, the methanol extraction protocol proved to be the best method. As a proof of utility, methanol protocol was then applied to milk samples from dairy cows fed a diet with or without a feed additive, showing a clear separation between the two groups of cows.

2019-06-13 | MTBLS623 | MetaboLights

Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes

Project description:Background: Canonical Nonsense Mediated Decay (NMD) is an important splicing-dependent process for mRNA surveillance in mammals. However, processed pseudogenes are not able to trigger NMD due to their lack of introns. It is largely unknown whether they have evolved other surveillance mechanisms. Results: Here, we find that the RNAs of pseudogenes, especially processed pseudogenes, have dramatically higher m6A levels than their cognate protein-coding genes, associated with de novo m6A peaks and motifs in human cells. Furthermore, pseudogenes have rapidly accumulated m6A motifs during evolution. The m6A sites of pseudogenes are evolutionarily younger than neutral sites and their m6A levels are increasing, supporting the idea that m6A on the RNAs of pseudogenes is under positive selection. We then find that the m6A RNA modification of processed, rather than unprocessed, pseudogenes promotes cytosolic RNA degradation and attenuates interference with the RNAs of their cognate protein-coding genes. We experimentally validate the m6A RNA modification of two processed pseudogenes, DSTNP2 and NAP1L4P1, which promotes the RNA degradation of both pseudogenes and their cognate protein-coding genes DSTN and NAP1L4. In addition, the m6A of DSTNP2 regulation of DSTN is partially dependent on the miRNA miR-362-5p. Conclusions: Our discovery reveals a novel evolutionary role of m6A RNA modification in cleaning up the unnecessary processed pseudogene transcripts to attenuate their interfering with the regulatory network of proteincoding genes.

2021-05-27 | GSE172219 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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