Senior Single-Cell RNA-Seq Scientist

Vertex Pharmaceuticals LLC; Boston (MA); On-site; USD 55,000 - 61,000; Full time

Benefits offered by this job

Healthcare benefits

Career development

Job summary

Vertex Pharmaceuticals LLC is seeking a Senior Research Associate to lead high-quality single-cell RNA sequencing sample processing and library preparation to support clinical research programs in a Boston-area setting.

The role requires deep hands-on expertise in single-cell workflows from tissue preparation to sequencing submission, with opportunities to influence experimental design, troubleshooting, and technology evaluation. Contract length: 12 months with potential extension.

Qualifications

• Bachelor’s degree in molecular biology or related field with 5+ years industry or academic lab experience; or Master’s with 2+ years.
• Hands-on NGS library preparation, preferably in single-cell RNA-sequencing workflows.
• Experience with single-cell platforms such as 10x Genomics Chromium, including GEM generation, cDNA amplification, library construction, and QC.
• Strong knowledge of RNA handling, molecular biology techniques, and practices to minimize sample loss, contamination, and variability.
• Experience preparing and assessing cell suspensions from primary cells and/or tissues.
• Strong organizational skills and ability to manage multiple experiments in a fast-paced environment.
• Ability to independently troubleshoot technical issues and communicate findings.

Responsibilities

• Plan, execute, document, and troubleshoot single-cell RNA-sequencing experiments using established and emerging single-cell genomics platforms.
• Perform cell and tissue dissociation, cell counting, viability assessment, enrichment, sorting coordination, cryopreservation, and sample preparation for single-cell assays.
• Generate high-quality single-cell suspensions from diverse sample types.
• Perform single-cell partitioning, barcoding, cDNA generation, amplification, and library preparation, including workflows such as 10x Genomics Chromium.
• Prepare libraries for gene expression and multiomic applications where applicable.
• Conduct routine quality-control assessments using Bioanalyzer, TapeStation, Fragment Analyzer, Qubit, qPCR, cell counters, and flow cytometry-based viability measurements.
• Prepare sequencing-ready libraries, coordinate sample submission with sequencing partners, and maintain sample metadata and chain-of-custody records.
• Partner with scientists, bioinformaticians, and project teams to translate questions into robust single-cell experimental plans.
• Advise on experimental variables including sample handling, cell recovery, sequencing depth, multiplexing strategy, batch design, and controls.
• Identify technical risks and recommend mitigations for challenging samples.
• Lead root-cause investigations for assay failures; implement CAPAs.
• Evaluate and validate new protocols, reagents, instruments, and automation to improve throughput and cost efficiency.

Skills

Single-cell RNA sequencing

10x Genomics Chromium

Cell isolation / dissociation

Library preparation

Troubleshooting

Education

Bachelor’s degree in molecular biology

Master’s degree in related field

Tools

Bioanalyzer

TapeStation

Fragment Analyzer

Qubit

qPCR

Flow cytometry

Job description

Vertex Pharmaceuticals LLC is seeking a Senior Research Associate to lead high-quality single-cell RNA sequencing sample processing and library preparation to support clinical research programs in a Boston-area setting.

The role requires deep hands-on expertise in single-cell workflows from tissue preparation to sequencing submission, with opportunities to influence experimental design, troubleshooting, and technology evaluation. Contract length: 12 months with potential extension.