TITLE: Pilot Exercise: Generating the Illumina SampleSheet and sharing data via BaseSpace
AUTHORS: Ruth  Timme, Maria   Balkey, Tunc Kayikcioglu, Candace Bias, Cameron Boerner, James Pettengill

[DESCRIPTION]
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.  

[STEPS]
SECTION: Generating Sequencing SampleSheet
1. 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 [ ].  Details for each section are described below. 

SECTION: Generating Sequencing SampleSheet
1.1. Header Section. 


 

SECTION: Generating Sequencing SampleSheet
1.2. Reads Section

**Enter the length of reads you are generating (could be different from 151)

 

SECTION: Generating Sequencing SampleSheet
1.3. Settings Section


 

SECTION: Generating Sequencing SampleSheet
1.4. 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.

         Sample_IDSample_NameSample_PlateSample_WellI7_Index_IDindexI5_Index_IDindex2Sample_ProjectDescriptionWPP-sample_B01sample_B01_M12341A1SU001TTGTTCCTTGI5_1CCGAACAACAPilotWPP-sample_C01sample_C01_M12341B1SU002AGGTTGTGTTI5_2AAGAATCGGCPilotWPP-sample_SA_101sample_SA_101_M12341C1SU003TATTGGTTGGI5_3CACTTCGCTTPilotWPP-sample_SA_201sample_SA_201_M12341D1SU004CACTTCGCTTI5_4TATTGGTTGGPilot
 
SECTION: Generating Sequencing SampleSheet
1.5. 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.  
SECTION: Generating Sequencing SampleSheet
2. 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.
SECTION: Transfer sequencing RUN through BaseSpace
3. Click the Runs tab in the Illumina BaseSpace website .

SECTION: Transfer sequencing RUN through BaseSpace
3.1. Select the run that you would like to share with the FDA LFFM wastewater project team.
SECTION: Transfer sequencing RUN through BaseSpace
3.2. Go to the summary tab and click at the share button.
SECTION: Transfer sequencing RUN through BaseSpace
3.3. Enter the email address for the FDA team (covidtrakr@fda.hhs.gov), and then click Add Collaborator.
SECTION: Transfer sequencing RUN through BaseSpace
3.4. Click Save Settings. Your run will be automatically shared with the FDA LFFM wastewater project team.

  



SECTION: Transfer sequencing PROJECT through BaseSpace
4. Click the Projects tab in the Illumina BaseSpace website .

SECTION: Transfer sequencing PROJECT through BaseSpace
4.1. Select the project that you would like to share with the FDA LFFM wastewater project team.
SECTION: Transfer sequencing PROJECT through BaseSpace
4.2. Click at the share project button.
SECTION: Transfer sequencing PROJECT through BaseSpace
4.3. Enter the email address for the FDA team (covidtrakr@fda.hhs.gov), and then click Add Collaborator.
SECTION: Transfer sequencing PROJECT through BaseSpace
4.4. Click Save Settings. Your project will be automatically shared with the FDA LFFM wastewater project team.