Jan 04, 2022
Version 3
Pilot Exercise: Generating the Illumina SampleSheet and sharing data via BaseSpace V.3
This protocol is a draft, published without a DOI.
- Ruth Timme1,
- Maria Balkey2,
- Tunc Kayikcioglu2,
- Candace Bias2,
- Cameron Boerner2,
- James Pettengill2
- 1US Food and Drug Administration;
- 2US Food And Drug Administration
- GenomeTrakrTech. support email: genomeTrakr@fda.hhs.gov
Protocol Citation: Ruth Timme, Maria Balkey, Tunc Kayikcioglu, Candace Bias, Cameron Boerner, James Pettengill 2022. Pilot Exercise: Generating the Illumina SampleSheet and sharing data via BaseSpace. protocols.io https://protocols.io/view/pilot-exercise-generating-the-illumina-samplesheet-b3gqqjvwVersion created by Maria Balkey
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it’s working
Created: January 04, 2022
Last Modified: January 04, 2022
Protocol Integer ID: 56560
Abstract
This protocol describes the required steps to generate Illumina SampleSheet and provides guidelines for sharing data via BaseSpace with FDA for the 2021 Pilot Exercise
V2:
- added more details regarding data transfer through BaseSpace, including steps for sharing a project with FDA-CFSAN.
- replaced samplesheet example.
V3:
- replaced samplesheet example.
Generating Sequencing SampleSheet
Generating Sequencing SampleSheet
Create your SampleSheet using Excel or a text editor. Name your sample sheet according your internal protocols, and use a *.csv extension. The sample sheet is organized in sections titled Header, Reads, Settings and Data. Section headings are case-sensitive and shown in brackets [ ]. 
SampleSheet.csv Details for each section are described below.
SampleSheet.csv Details for each section are described below. Header Section.
| A | B | |
| Parameter | Description | |
| Investigator Name | First Name and Last Name for laboratory scientist | |
| Experiment Name | Pilot Exercise SARS-Cov-2 | |
| Date | YYYY-MM-DD | |
| Workflow | GenerateFASTQ | |
| Application | FASTQ Only | |
| Instrument Type | MiSeq | |
| Library Prep Kit | Swift Normalase Amplicon NGS Panels (SNAP) | |
| Index Kit | Swift Normalase Amplicon NGS Panels (SNAP) | |
| Description | FDA Wastewater Protocol Pilot Exercise | |
| Chemistry | Amplicon |
Table 1: Header Section in Sequencing SampleSheet
Reads Section
**Enter the length of reads you are generating (could be different from 151)
| A | B | |
| Parameter | Description | |
| Number of cylces in Read 1 | 151 | |
| Number of cycles in Read 2 | 151 |
Table 2: Reader Section in Sequencing SampleSheet
Settings Section
| A | B | |
| ReverseComplement | 0 |
Table 3: Settings Section in Sequencing SampleSheet
Data Section: Include the machine ID in the Sample_Name column. e.g. sample_B01_M01234 where M01234 corresponds to the machine ID. This is the ID that will get populated to the fastq file names.
| A | B | C | D | E | F | G | H | I | J | |
| Sample_ID | Sample_Name | Sample_Plate | Sample_Well | I7_Index_ID | index | I5_Index_ID | index2 | Sample_Project | Description | |
| WPP_sample_B.01 | WPP_sample_B.01_M01234 | 1 | A1 | SU001 | TTGTTCCTTG | I5_1 | CCGAACAACA | LabAbreviation-WPP | ||
| WPP_sample_C.01 | WPP_sample_C.01_M01234 | 1 | B1 | SU002 | AGGTTGTGTT | I5_2 | AAGAATCGGC | LabAbreviation-WPP | ||
| WPP_sample_SA-1.01 | WPP_sample_SA-1.01_M01234 | 1 | C1 | SU003 | TATTGGTTGG | I5_3 | CACTTCGCTT | LabAbreviation-WPP | ||
| WPP_sample_SA-2.01 | WPP_sample_SA-2.01__M01234 | 1 | D1 | SU004 | CACTTCGCTT | I5_4 | TATTGGTTGG | LabAbreviation-WPP |
Table 4: Data Section in Sequencing SampleSheet (dashes converted to underscores for Illumina requirements)
If a new library or sequencing protocol is utilized for processing the pilot exercise samples, make the changes in the corresponding parameters for the sequencing sample sheet.
Starting your MiSeq run and connecting to BaseSpace:
When you set up the run on the MiSeq, select the option to log in to BaseSpace.
Transfer sequencing RUN through BaseSpace
Transfer sequencing RUN through BaseSpace
Click the Runs tab in the Illumina BaseSpace website .
Select the run that you would like to share with the FDA LFFM wastewater project team.
Go to the summary tab and click at the share button.
Enter the email address for the FDA team (covidtrakr@fda.hhs.gov), and then click Add Collaborator.
Click Save Settings. Your run will be automatically shared with the FDA LFFM wastewater project team.
Figure 1: Sharing data via BaseSpace by Email Invitation
Transfer sequencing PROJECT through BaseSpace
Transfer sequencing PROJECT through BaseSpace
Click the Projects tab in the Illumina BaseSpace website .
Select the project that you would like to share with the FDA LFFM wastewater project team.
Click at the share project button.
Enter the email address for the FDA team (covidtrakr@fda.hhs.gov), and then click Add Collaborator.
Click Save Settings. Your project will be automatically shared with the FDA LFFM wastewater project team.