RNA Extraction from Wastewater Concentrates Using RNeasy and Zymo Kits v1

2021 ◽  
Author(s):  
Jacquelina.Woods not provided ◽  
rachel.rodriguez not provided
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Wastewater Collection

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This method describes the extraction of RNA from viral concentrates using the RNeasy and Zymo kits.

6M GITC v1

2021 ◽  
Author(s):  
Jacquelina.Woods not provided
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Wastewater Collection

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This method provides a reagent formula required in the extraction of RNA from viral concentrates using the RNeasy and Zymo kits.

2X PEG v1

2021 ◽  
Author(s):  
Jacquelina.Woods not provided
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Wastewater Collection

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This method provides a reagent formula required in the rapid concentration of intact viruses from wastewater using a combination of PEG precipitation and ultracentrifugation.

0.05 M Glycine v1

2021 ◽  
Author(s):  
Jacquelina.Woods not provided
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Wastewater Collection

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This method provides a reagent formula required in the rapid concentration of intact viruses from wastewater using a combination of PEG precipitation and ultracentrifugation.

Tissue Culture (tc) PBS v1

2021 ◽  
Author(s):  
Jacquelina.Woods not provided
Keyword(s):  
Tissue Culture ◽  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Wastewater Collection

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This method provides a reagent formula required in the rapid concentration of intact viruses from wastewater using a combination of PEG precipitation and ultracentrifugation.

Virus Concentration from Wastewater Using PEG Precipitation and Ultracentrifugation v1

2021 ◽  
Author(s):  
Jacquelina.Woods not provided ◽  
rachel.rodriguez not provided
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Rna Extraction ◽  
Virus Concentration ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Wastewater Collection

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This method describes the rapid concentration of intact viruses from wastewater using a combination of PEG precipitation and ultracentrifugation.

Primer TE (10mM Tris, 0.1mM EDTA, pH8.0) v1

2021 ◽  
Author(s):  
Jacquelina.Woods not provided
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Wastewater Collection

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This method provides a reagent formula required in the extraction of RNA from viral concentrates using the RNeasy and Zymo kits.

5N HCl v1

2021 ◽  
Author(s):  
Jacquelina.Woods not provided
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Wastewater Collection

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This method provides a reagent formula required in the rapid concentration of intact viruses from wastewater using a combination of PEG precipitation and ultracentrifugation.

NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Maria Balkey
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Sequence Data ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Set Up

PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater; however, this protocol was written to be broadly applicable for all wastewater sequence data submissions to NCBI. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This protocol covers the last step of making your data public at NCBI. Specifically, it provides the steps to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 in this protocol to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. Version updates: V2: minor edits to the BioSample and SRA templates V3: Many minor edits were made to make the protocol more broadly applicable to submitters outside of FDA's wastewater project. Updates were also made to both metadata templates, including a new attribute to the SRA metadata template, called "enrichment_kit". There are now three custom attributes we recommend populating to more specifically capture relevant methods for ww sequencing: enrichment approach, primer set, and library prep kit.

NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Maria Balkey
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Large Volume ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Set Up

PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This protocol covers the last step of making your data public at NCBI. Specifically, it provides the steps to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 in this protocol to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. Version updates: V2: minor edits to the BioSample and SRA templates

NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject v1

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Maria Balkey
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Large Volume ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Set Up

PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This protocol covers the last step of making your data public at NCBI. Specifically, it provides the steps to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 in this protocol to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API.

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