Thais' notebook BSB genomics
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Sample locations are in the -80oC freezer inventory
- filter for
Owner
==Thais
- BSB_NC_Box Fin clips OGL Buffer
- BSB_SMC_ME_Box Fin clips (buffer?)
- BSB_MD_Box fin clips in OGL buffer
- BSB_NJ_BOX Fin clips in OGL buffer
- filter for
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Black sea bass shared datasheet
- First tab:
Fin_Clip_Vial_ID
is the vial ID - Tab:
selected for genomics
has 64 samples that Thais extracted last March, Thais thinks the extracts are in the boxes in the -80C (even though these boxes say tissue, she thinks they are the extracts).- BSB_NC_Box Fin clips OGL Buffer
- BSB_SMC_ME_Box Fin clips (buffer?)
- BSB_MD_Box fin clips in OGL buffer
- BSB_NJ_BOX Fin clips in OGL buffer
- remaining samples
- ~20-25 samples from RI in the freezer - Katie thinks this is the box in the -20C
- we need to check the length data, but we can extract all these
- Marissa has <10 samples from ME
- waiting to receive them from Marissa
- ~20-25 samples from RI in the freezer - Katie thinks this is the box in the -20C
- First tab:
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- Up to March 12, was troubleshooting
- Unique_ID is what is used to match to datasheet
- 20201118 Thais made some changes to the entry 2020-01-BSB-DNA-extraction_summary.md to clarify dilution factors used to measure sample concentrations using Qubit and to provide a separate table listing the 62 extracted samples to be sent out to sequencing facility.
- 20201118 Thais fixes some typos in the notebooks (diddn't change anything regarding number of samples or DNA quants).
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Sequencing facility contact info:
- "We request DNA to be sent with volumes >20 ul and concentrations >25 ng/ul as measured by Picogreen or Qubit since Nanodrop will tend to overestimate the amount of double stranded DNA available. However, we input 10 ul of DNA at 10 ng/ul into our GBS library preparation, so DNA >10 ng/ul as measured by Picogreen or Qubit is acceptable. Our library prep rate includes an initial Picogreen QC step, and we can still attempt library prep on sequencing on samples with concentrations <10 ng/ul. We have successfully sequenced samples with initial concentrations <5 ng/ul, however, the results are more variable and we cannot guarantee that the samples will be successful."
- Email: Evan Forsberg GBS Service Manager 1-202 NHH 312 Church St SE Minneapolis, MN 55455 (612) 624-3177 [email protected]
- Thais will forward correspondence to Katie and Alan - DONE (TB).
- Budget: ~$7000-$9000
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- May need to purchase another kit (~$1000)
- May also needd to purchase quantification kits (Qubit or Picogreen)
- E.Z.N.A tissue DNA kit (D3396-02, Omega) - tubes (T) method
- if we use plates, may need to go to Randall's lab
- Use elution volume less of what they tell you to do (~30uL instead of 100uL for first elution and 70uL out of second elution), stored separately and not combined. Thais checked 2nd elution and not much there.
- Sara used to use 1/2 the elution volume for her samples, then she combined them
TO DO:
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Sample summary
- RI samples (southern new england) - data not organized
- Sample location is our freezer
- 22 to extract/sequence
- MA samples from Sept 2020 - where are these stored?
- Thais gave EtOH vials to them
- Tommy and Jonathon collected and processed them on the boat
- In door of standing -20C freezer in Grabowski Lab
- 20-30: extract as many as we can that are less than 30
- NJ "conflict" - no date? Fixed with Jon/thais
- thais has a spreadsheet that came with these samples
- NC samples - no date? Fixed with Jon/thais
- ME list - this is a list of vials that Thais sent to Marissa, but never sent back to us
- Thais says that Marissa didn't enter information to big spreadsheet - Thais made a separate one
- thais will enter details - June and Nov 2020
- 15 samples, 9 are smaller than 30cM and 2 marked as YOY
- Jon will get Marissa to send the finclips
- RI samples (southern new england) - data not organized
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Sample summary extracted by Thais (62 samples)
- NJ 17
- MD 20
- Seouthern NE 7
- ME 5
- NC 13
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Katie
- Confirm all samples with Jon
- Get remaining finclips and data from ME - Marissa
- Quotes from sequencing facility
quote ddRAD library prep and sequencing
email thread - Data quality control - we're not sure if these data are entered yet
- thais entered vial IDs for Maine samples, because she setn to Marissa
- thais entered vial IDs for RI/MA samples, because she setn to Jon
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Thais: Go through data in this spreadsheet and transfer to the Black sea bass shared datasheet. DONE (TB)
- Thais will move this data into the database DONE (TB)
- Thais thinks we can sequence all of them (all 62 listed above, TB)
- Notes in right column are based on concentration and volume:
- plenty: for all samples which we have quantity from Sequencing facility
- acceptable, could retry: we have enough, but the concentrations are greater than 5 and less than 25ng/uL
repeated
had to extract twice, some samples we have less than 5
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Alan: extractions
- extract remaining samples
- quantify all samples we plan to send to sequencing on plate reader
- prepare for sequencing requried by sequencing facility
- help with shipping to sequencing facility