Metagenome sequencing raw data
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA886109 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21778113_1.fastq.gz | Fastqsanger.gz | |||
| SRR21778113_2.fastq.gz | Fastqsanger.gz | |||
| SRR21778114_1.fastq.gz | Fastqsanger.gz | |||
| SRR21778114_2.fastq.gz | Fastqsanger.gz | |||
| SRR21778115_1.fastq.gz | Fastqsanger.gz |
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Project description:Whole genome/exome sequencing (WGS/WES) has become widely adopted in research and, more recently, in clinical settings. Many hope that the information obtained from the interpretation of these data will have medical benefits for patients and-in some cases-also their biological relatives. Because of the manifold possibilities to reuse genomic data, enabling sequenced individuals to access their own raw (uninterpreted) genomic data is a highly debated issue. This paper reports some of the first empirical findings on personal genome access policies and practices. We interviewed 39 respondents, working at 33 institutions in 21 countries across Europe. These sequencing institutions generate massive amounts of WGS/WES data and represent varying organisational structures and operational models. Taken together, in total, these institutions have sequenced ?317,259 genomes and exomes to date. Most of the sequencing institutions reported that they are able to store raw genomic data in compliance with various national regulations, although there was a lack of standardisation of storage formats. Interviewees from 12 of the 33 institutions included in our study reported that they had received requests for personal access to raw genomic data from sequenced individuals. In the absence of policies on how to process such requests, these were decided on an ad hoc basis; in the end, at least 28 requests were granted, while there were no reports of requests being rejected. Given the rights, interests, and liabilities at stake, it is essential that sequencing institutions adopt clear policies and processes for raw genomic data retention and personal access.
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Project description:In the early stages (30 days) of phosphorus deficiency stress, Epimedium pubescens leaves cope with short-term phosphorus deficiency by increasing the expression of related genes such as carbon metabolism, flavonoid synthesis and hormone signal transduction pathways, producing sufficient energy, scavenging ROS, and adjusting plant morphology. However, with the extension of stress duration to 90 days, the expression of genes related to phosphorus cycling and phosphorus recovery (PHT1-4, PHO1 homolog3, PAP) was upregulated, and transcriptional changes and post-transcriptional regulation (miRNA regulation and protein modification) were enhanced to resist long-term phosphorus deficiency stress. In addition, bHLH, MYB, NAC, WRKY and other families also play an important role in regulating gene expression and coping with phosphorus deficiency stress, especially MYB60 negatively regulates flavonoid synthesis pathway, which is significantly down-regulated in leaves treated with phosphorus deficiency for 30 days, thereby promoting the accumulation of flavonoid compounds in leaves.
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Project description:The hBMEC CRISPR/Cas9 library was seeded in eight T225 flasks with 2 × 107 cells each and incubated for 3 days. The hBMECs doubled every 3 days, generating a total of 3.2 × 108 cells, which were divided into four parts, yielding 8 × 107 cells per experimental condition (~1,000× coverage per perturbation in each library). A quarter of the cells were used as the input library and the remaining three quarters for SzM cytotoxicity screens. The cell libraries were treated with purified SzM protein diluted in DMEM (10% FBS) at a final concentration of 50 μg/ml for 48 hr; when ~50% cells were dead, the surviving cells were out grown in fresh DMEM (10% FBS) without SzM protein. These cells were divided into two parts, one part for genomic DNA extraction, and the other for the next round of screening. The same treatment with 50 μg/ml purified SzM protein for 48 hr was used in the 2nd round and the 3rd rounds, using the same protocol outlined above. After the 3rd round, all cells were harvested for genomic DNA extraction.
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