Amanda Raine

upSPLAT: Early-Barcoded Library Preparation for Cost-Effective Population-Scale Genomics

upSPLAT reduces library preparation costs by 10-fold through early barcoding and single-stranded ligation, enabling cost-effective, high-plex sequencing across diverse DNA inputs.

Circulating cell-free RNA reflects inflammatory and airway remodeling signatures in an equine model of asthma

The paper analyzes circulating cell-free RNA from asthmatic and healthy horses to identify inflammatory and airway remodeling signatures, showing its potential as a biomarker for asthma.

Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells

This study evaluates the HIVE scRNA-seq method for processing equine BAL cells, finding it identifies major cell types but underrepresents T cells and overrepresents macrophages, with potential for improvement.

Mapping the Spatial Proteome of Leukemia Cells Undergoing Fludarabine Treatment

This study uses spatial proteomics to analyze changes in leukemia cell surface proteins after fludarabine treatment, identifying proteins and interactions that may contribute to chemotherapy resistance.

COMPARISON OF HIGH-THROUGHPUT SINGLE-CELL RNA-SEQ METHODS FOR EX VIVO DRUG SCREENING

The paper compares three scRNA-seq methods for ex vivo drug screening in ALL cells, finding consistent transcriptional responses to fludarabine despite method-specific differences.

Single cell transcriptomics delineates the immune-cell landscape in equine lower airways and reveals upregulation of the FKBP5 gene in horses with asthma

The paper uses scRNA-seq to analyze immune cell populations in equine BAL fluid from horses with asthma and healthy controls, identifying FKBP5 as upregulated in asthma cases.

An equine Endothelin 3 cis-regulatory variant links blood pressure modulation to elite racing performance

This paper identifies a cis-regulatory variant near EDN3 linked to blood pressure regulation and elite racing performance in horses.

scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation

scSPLAT improves single-cell WGBS library preparation by increasing scalability and read alignment rates compared to existing methods.

The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

The paper evaluates epigenetic methods using reference materials, finding high concordance between assays and differences in performance across platforms.

Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing

This study uses linked-read whole genome sequencing to detect and phase structural aberrations in pediatric ALL with higher resolution than traditional methods.

Data quality of Whole Genome Bisulfite Sequencing on Illumina platforms

The paper assesses WGBS data quality on HiSeq X, HiSeq 2500, and NovaSeq systems, finding improved quality after software upgrades.