QueryFuse
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB34715 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3572800.fastq.gz | Fastqsanger.gz | |||
| ERR3572810.fastq.gz | Fastqsanger.gz | |||
| ERR3572801.fastq.gz | Fastqsanger.gz | |||
| ERR3572811.fastq.gz | Fastqsanger.gz | |||
| ERR3572802.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
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Project description:Prior to the introduction of novel food ingredients into the food supply, safety risk assessments are required, and numerous prediction models have been developed and validated to evaluate safety. The allergenic risk potential of Helaina recombinant human lactoferrin (rhLF, Effera™), produced in Komagataella phaffii (K. phaffii) was assessed by literature search, bioinformatics sequence comparisons to known allergens, glycan allergenicity assessment, and a simulated pepsin digestion model. The literature search identified no allergenic risk for Helaina rhLF, K. phaffii, or its glycans. Bioinformatics search strategies showed no significant risk for cross-reactivity or allergenicity between rhLF or the 36 residual host proteins and known human allergens. Helaina rhLF was also rapidly digested in simulated gastric fluid and its digestibility profile was comparable to human milk lactoferrin (hmLF), further demonstrating a low allergenic risk and similarity to the hmLF form. Collectively, these results demonstrate a low allergenic risk potential of Helaina rhLF and do not support the need for further clinical testing or serum IgE binding to evaluate Helaina rhLF for risk of food allergy prior to addition into the food supply.
2024-10-17 | PXD053985 | Pride
Project description:This submission includes the sample data for a protocol covering differential expression analysis with TopHat and Cufflinks. The protocol also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-Seq analysis results. While the procedure assumes basic informatics skills, these tools assume little to no background with RNA-Seq analysis and are meant for novices and experts alike. The protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results. The example data was generated in silico to closely resemble a real experiment in Drosophila melanogaster. First, expression values in cultured S2 cells were calculated for FlyBase 5.2 transcripts. These values were used to generate 3 sequencing replicates for condition "C1", with underlying variability in expression across replicates simulated by fitting a negative binomial model through the real S2 read count data. A second simulated condition "C2" was generated by perturbing expression for 300 randomly selected genes. Genes were perturbed by selecting the most highly expressed isoform and increasing its relative expression by three fold. Three replicates of this condtion were sequenced as above. Simulated sequencing was performed by picking a transcript from the FlyBase transcriptome with equal to its abundance, choosing a fragment length from a normal distribution with mean = 180bp and standard deviation = 20bp, and then choosing a start point for the fragment within the transcript uniformly at random. Total sequencing yield for each replicate was chosen to match that of the real S2 data. Each replicate was mapped to the fly genome with TopHat v 1.3.1 seperately. The replicates were assembled seperately with Cufflinks v 1.1.0. The replicate assemblies were merged with Cuffmerge. This merged assembly was then analysed for differentially expressed and regulated genes with Cuffdiff.
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