---
title: "Re-extraction of low-quantity samples"
author: "Kathleen Durkin"
date: "2025-07-15"
categories: ["SIFP_2025"]
format:
  html
bibliography: ../../../references.bib
---

Several of the older samples had low DNA concentrations (\<10ng/uL) (see [quantification notes](./2025_07_14_qubit.qmd) for details). To obtain enough DNA for library prep (\>= 400ng), I need to extract more DNA from these specimens.

To do this, I'll do several extractions for each of the specimens, then pool each specimen's extractions before Zymo Cleanup to concentrate the multiple extractions into one higher-concentration elution.

### Subsampling

**USNM 14366\
USNM 19054\
USNM 52295\
USNM 1180630\
USNM 50603**

For each of the above specimens, subsampled 4 times as described in the subsampling protocol provided in my [July 9 post](./2025_07_09_subsampling_extractions.qmd). Each set of subsamples was labelled with the catalog number and then A, B, C, or D.

During subsamplling I was able to see where on the specimen I had previously sampled tissue. I subsampled this time from the same stalk/finger, to preserve the undamaged portions of the specimens.

### Tissue digestion

Digested the above specimens (20 total) as detailed in the **Digestion Protocol** in my [July 9 post](./2025_07_09_subsampling_extractions.qmd).

Digestions began incubating at 3:00pm, 07/15/25.

### Extraction

Pulled digesting tissue from shaking incubators at 1:00pm, 07/17/2025, and finished extraction as detailed in the **Qiagen Extraction Protocol** included in my [July 11 post](./2025_07_11_extractions.qmd).