search

urol-e5 / timeseries

Data generated from e5 time series sampling in Moorea
2 stars 0 forks source link

Process remaining samples for E5 time series species identification #65

Closed AHuffmyer closed 3 months ago

AHuffmyer commented 4 months ago

This issue contains all the information needed to process the remaining E5 time series samples for species identification.

Pocillopora samples

Sample Marker
POC-200 POC Histone
POC-205 POC Histone
POC-207 POC Histone
POC-215 POC Histone
POC-217 POC Histone
POC-238 POC Histone
POC-239 POC Histone
POC-248 POC Histone
POC-254 POC Histone
POC-366 POC Histone
POC-386 POC Histone
POC-395 POC Histone
POC-41 POC Histone
POC-45 POC Histone
POC-55 POC Histone

We now need to conduct PCR/RFLP for POC Histone to distinguish between P. meandrina and P. grandis. See links below for protocols and primers. Please amplify these samples for the POC Histone marker and proceed with the POC Histone RFLP. See links below.

Porites Samples

Sample Marker
POR-362 Reamplify and resequence for H2
POR-83 Reamplify and resequence for H2

These samples failed sequencing previously. See links below for protocols and primers and reamplify and send these samples for Sanger sequencing.

Protocols, primers, and notebook posts

PCR protocol and primers for POC Histone and POR H2 is located in Zoe's notebook post here

Previous PCR and Sequencing information is located in Zoe's notebooks posts here and here. Protocol also available in Hollie's notebook here.

Please first read through these protocols and notebook posts to familiarize yourself with the work that has been completed and the protocols. Then please proceed with amplification and sequencing for the samples listed above.

POC Histone RFLP is detailed in Johnston et al. 2018 and in Hollie's notebook here.

Please detail your procedures in notebook posts and upload any data to the E5 time series GitHub Species ID folder.

Please complete these steps by the end of March, or as soon as possible.

AHuffmyer commented 3 months ago

@hputnam should we do both sequencing for POC Histone and RFLP? Or do you recommend only sequencing from the last set of identifications that you did?

AHuffmyer commented 3 months ago

Above comment resolved. We need forward sequencing for mtORF for Pocillopora and PCR + RFLP For Pocillopora POC Histone

daniellembecker commented 3 months ago

Finding all samples, primers, and supplies necessary for these approaches this week! Then I will be doing the PCR/RFLP for POC Histone on Monday the 25th and then reamplify POR H2 on Thursday the 28th!

AHuffmyer commented 3 months ago

Great! And I’ll be at URI during that time so I can help/learn!

AHuffmyer commented 3 months ago

Once processing is done we need to add information to this spreadsheet: https://docs.google.com/spreadsheets/d/1NbWRAi-Ko7zgQqbTuAFRxV7qBS_E6AaXG0XdwiSJ-lA/edit#gid=152104885

and add species ID to these sheets: https://github.com/urol-e5/timeseries/tree/master/time_series_analysis/Species_ID

AHuffmyer commented 3 months ago

Completed https://ahuffmyer.github.io/ASH_Putnam_Lab_Notebook/E5-POC-and-POR-Species-ID-PCR-and-RFLPs/