RNAseq analysis of gene counts and expression levels in diabetic foot ulcers

In this study we examine the temporal changes in the transcriptome of chronic wounds to identify dynamic differences between healing and non-healing wounds. Wound tissue samples were collected over a 12-week period from human subjects with chronic, diabetic foot ulcers. Some healed during the observation period, and some remained unhealed. Bulk RNAseq analysis was performed to find differences in dynamic patterns., Seventeen patients, 18+ years from Northern California VA Medical Center (Mather, CA) with a diabetic foot ulcer that had not improved > 50% for 4+ weeks, were enrolled in the study from 2021 to 2022. Wounds were monitored over 12 weeks to classify them as \"healers\" or \"non-healers\". Tissue from wound margins was collected during the standard of care and debridement, and preserved in RNALater (Life Tech). Tissue samples were homogenized, total RNA was extracted with the Quick-RNA Mag Bead kit (Zymo Research), and the integrity of the RNA was evaluated using an Agilent Tape Station (Agilent). For sequencing, indexed libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v3 (Takara Bio). Both the quantity and quality of these libraries were appraised by a Qubit fluorometer and an Agilent 2100 bioanalyzer. Molar concentrations of the libraries were confirmed by qPCR prior to pooling. The sequencing process was conducted on the Illumina NovaSeq 6000 platform, utilizing P..., , # RNAseq analysis of gene counts and expression levels in diabetic foot ulcers

[https://doi.org/10.5061/dryad.2v6wwpzzc](https://doi.org/10.5061/dryad.2v6wwpzzc)

## Principle Investigator Contact Information:

Name: Rivkah Isseroff

Institution: University of California, Davis

Email: [[e-mail]](mailto:[e-mail])

## Dataset Overview

Temporal wound tissue was collected from 17 patients with a diabetic foot ulcer at Northern California VA Medical Center (Mather, CA) between 2021 and 2022. Wounds were monitored over 12 weeks to classify them as \"healers\" or \"non-healers\" (please see \"Patients.xlsx\" for the sample information.). Tissue from wound margins was collected during the debridement of wound care, and preserved in RNALater (Life Tech). Tissue samples were homogenized, total RNA was extracted for RNAseq. To map to the human genome, The Cogent NGS analysis pipeline (CogentAP) from Takara Bio (v2.0) was used to de-multiplex and analyze each fastq file. Th..., In the approved IRB protocol, no patient consent was needed for the discarded tissue as these are non-consent requiring procedures routinely performed in the clinics by both nurses and physicians.

The discarded tissue was de-identified during the collecting process and kept in numbered tubes without PHI information for lab analysis.