Nuclei Isolation Protocol Validation for Rat and Cow White Adipose Tissue

A 483.7 KB document details the validation and optimization of a nuclei isolation protocol for single-nucleus RNA sequencing of white adipose tissue from Dahl Salt Sensitive rats and cattle. The study reports optimized yields of 3,100 nuclei/mg tissue from rat retroperitoneal fat and 2,050 nuclei/mg from cow white fat, but notes low median gene counts in rat tissues. Authored by Janice M. Thompson and posted on figshare in March 2026.

Use Cases

• Compare nuclei yield metrics (nuclei/mg tissue) across rat retroperitoneal fat, rat mesenteric PVAT, and cow white fat to evaluate protocol efficacy.
• Analyze transcriptomic data quality by comparing median genes per cell (1,720 for cow vs. 189-294 for rat) to assess species-specific challenges.
• Validate a modified nuclei isolation protocol incorporating liquid nitrogen pulverization and Dounce homogenization for flash-frozen WAT samples.
• Identify biological differences in adipose depots by correlating nuclei yield and gene detection metrics with species (rat, cow) and depot type (perivascular, non-perivascular).

Strengths

• Provides specific quantitative metrics for protocol evaluation: nuclei yield per mg of tissue (e.g., 3,100 for rat RP fat) and median genes per cell (e.g., 1,720 for cow).
• Compares results across two relevant animal models (rat and cattle) and multiple adipose tissue depots (perivascular and non-perivascular).
• Documents a clear methodological challenge and optimization process for a specific application in genomics.

Limitations

• The dataset is a small 483.7 KB document describing a study, not a primary sequencing data repository, limiting direct analytical use.
• Reported transcriptomic data quality for rat WAT depots is very low (189-294 median genes/cell), hindering downstream bioinformatic analysis.
• No primary columnar data or sample-level records are provided, only summarized results and methodological descriptions.

Provenance

Source

Janice M. Thompson via figshare.

Collection Method

Experimental validation and optimization of a nuclei isolation protocol, evaluated via microscopic visualization and single-nucleus RNA sequencing.

Freshness

Last updated March 2026.