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ID Oly Gonad Samples for RNA-Seq #631

Closed sr320 closed 7 years ago

sr320 commented 7 years ago

Need 4-9 low pH samples and 4-9 control samples...

laurahspencer commented 7 years ago

Here are my thoughts:

Ideally I'd like to run samples from both North Sound and South Sound, and a male, female, and hermaphrodite from each of the low pH and ambient pH groups. I assume these won't be pooled? If we do 3 samples from each site/treatment, one per sex (no rep), they are as follows:

SN low pH

  1. male
  2. female
  3. hermaphrodite

SN ambient pH

  1. male
  2. female
  3. hermaphrodite

NF low pH

  1. male
  2. female
  3. hermaphrodite

NF ambient pH

  1. male
  2. female
  3. hermaphrodite

What do you guys think? We can narrow down the site/sex by either doing only South Sound, or not using hermaphroditic individuals. I'll use Katie's images of the histology slides to ID sex and generous presence of gonad.

sr320 commented 7 years ago

Are their gonad samples in -80 that correspond to slides? IOW do we extract from tubes or histo cassettes?

laurahspencer commented 7 years ago

I only have go ad samples fixed in the histology cassettes. In the freezer at Manchester I have ctenidia, mantle, and adductor, and I also have excess tissue in ethanol.

On Wed, Jun 28, 2017 at 9:40 AM Steven Roberts notifications@github.com wrote:

Are their gonad samples in -80 that correspond to slides? IOW do we extract from tubes or histo cassettes?

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sr320 commented 7 years ago

Images are at https://drive.google.com/drive/u/1/folders/0B6vcfZRVqdYHUVQ0ZmZ3VTlpYkU

for sex determination of individuals

laurahspencer commented 7 years ago

Any input on the # of each sex/location? Should we loop in Katherine?

If we move forward with the below, here are sample ID's, and the histology key for reference (We should work with Katie to make sure we sample the correct tissue in each cassette). I've selected all from the "overwintered" temp of 10degC, since their gonads appeared more developed than the 6degC.

SN low pH

  1. male - SN-10-20
  2. female - SN-10-16
  3. hermaphrodite - SN-10-17

SN ambient pH

  1. male - SN-10-25
  2. female - SN-10-31
  3. hermaphrodite - SN-10-26

NF low pH

  1. male - NF-10-24
  2. female - NF-10-23
  3. hermaphrodite - NF-10 22

NF ambient pH

  1. male - NF-10-28 (not 100% male, a few oocytes)
  2. female - NF-10-30
  3. hermaphrodite - NF-10-26
sr320 commented 7 years ago

It will be two pools, Ambient and low pH. This is designed as reference that could later be used for tag-seq for individual gene expression.

On Wed, Jun 28, 2017 at 2:54 PM laurahspencer notifications@github.com wrote:

Any input on the # of each sex/location? Should we loop in Katherine?

If we move forward with the below, here are sample ID's, and the histology key https://laurahspencer.github.io/LabNotebook/Prepping-Histology-Samples/ for reference (We should work with Katie to make sure we sample the correct tissue in each cassette). I've selected all from the "overwintered" temp of 10degC, since their gonads appeared more developed than the 6degC.

SN low pH

  1. male - SN-10-20
  2. female - SN-10-16
  3. hermaphrodite - SN-10-17

SN ambient pH

  1. male - SN-10-25
  2. female - TBD; still need images from SN-10-27 through 33
  3. hermaphrodite - SN-10-26

NF low pH

  1. male - NF-10-24
  2. female - NF-10-23
  3. hermaphrodite - NF-10 22

NF ambient pH - (missing image for NF-10-25)

  1. male - NF-10-28 (not 100% male, a few oocytes)
  2. female - NF-10-30
  3. hermaphrodite - NF-10-26

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sr320 commented 7 years ago

@laurahspencer More images were taken today can you see if you can decide on

  1. female - TBD; still need images from SN-10-27 through 33
laurahspencer commented 7 years ago

whoops - moved this comment to the appropriate issue

Updated my previous comment. @kubu4, you'll probably want to work with Katie to make sure that you're extracting from the same sample as the one she imaged. The histology folks did not keep the samples in the same formation. Katie used my images of the prepared cassettes and my histology "map" to ID each sample.