Senior Research Associate, Single-Cell RNA Sequencing (Contract)

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

Job Description

We are seeking a highly skilled and motivated Senior Research Associate to join our analytical development molecular biology team. This role will lead and execute high-quality single-cell RNA sequencing (scRNA-seq) sample processing and library preparation to support clinical research programs.

The successful candidate will bring deep hands-on expertise in single-cell workflows—from tissue and cell preparation through library construction, quality control, and sequencing submission—and will serve as a technical resource for experimental design, troubleshooting, workflow optimization, and technology evaluation. The level of hire will be determined by the candidate’s depth of experience, technical leadership, and demonstrated ability to independently drive complex projects.

Key Responsibilities:

Single-Cell Experiment Execution

• Independently 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 a range of sample types, including cultured cells, primary cells, blood-derived samples, and tissues.
• Perform single-cell partitioning, barcoding, cDNA generation, amplification, and library preparation, including workflows such as 10x Genomics Chromium and related platforms.
• Prepare libraries for gene expression and, where applicable, multiomic applications such as cell-surface protein profiling, immune-repertoire profiling, chromatin accessibility, or spatial/transcriptomic workflows.
• Conduct and interpret routine quality-control assessments using instruments and methods such as Bioanalyzer, TapeStation, Fragment Analyzer, Qubit, qPCR, cell counters, and flow cytometry-based viability measurements.
• Prepare sequencing-ready libraries, coordinate sample submission with internal or external sequencing partners, and maintain complete sample metadata and chain-of-custody records.

Experimental Design and Technical Leadership

• Partner with scientists, bioinformaticians, and project teams to translate scientific questions into robust single-cell experimental plans.
• Advise on experimental variables including sample handling, cell recovery, target cell numbers, sequencing depth, multiplexing strategy, batch design, and appropriate controls.
• Identify technical risks early and recommend practical mitigations for challenging samples, including low-input, low-viability, frozen, fibrotic, or highly heterogeneous tissues.
• Lead root-cause investigations for assay failures or unexpected quality outcomes; implement corrective and preventive actions.
• Evaluate, optimize, and validate new protocols, reagents, instruments, and automation opportunities to improve throughput, reproducibility, sample quality, and cost efficiency.
• Contribute to the development of standardized operating procedures, assay qualification plans, training materials, and best practices.

Collaboration, Documentation, and Operations

• Maintain clear, contemporaneous experimental records in electronic laboratory notebooks and laboratory information management systems, as applicable.
• Analyze and communicate laboratory QC data, experimental outcomes, and technical recommendations clearly to cross-functional stakeholders.
• Present results, assay performance trends, and technical updates at team meetings and project reviews.
• Manage inventory, reagent qualification, instrument maintenance, and laboratory readiness for single-cell workflows.
• Train, mentor, and provide day-to-day technical guidance to junior team members, as appropriate.
• At the Principal level, help define platform strategy, establish scalable operational capabilities, and influence scientific direction across multiple programs.

Required Qualifications:

• Senior RA: Bachelor’s degree in molecular biology, cell biology, genomics, biotechnology, or a related scientific discipline, with 5+ years of relevant industry or academic laboratory experience; or a Master’s degree with 2+ years of relevant experience.
• Demonstrated hands-on experience performing next-generation sequencing library preparation, preferably in single-cell RNA-sequencing workflows.
• Experience with single-cell platforms such as 10x Genomics Chromium, including cell preparation, GEM generation, cDNA amplification, library construction, and QC.
• Strong knowledge of RNA handling, molecular biology techniques, and practices required to minimize sample loss, contamination, and technical variability.
• Experience preparing and assessing cell suspensions from primary cells and/or tissues.
• Strong organizational skills, attention to detail, and ability to manage multiple experiments in a fast-paced, collaborative environment.
• Ability to independently troubleshoot technical issues and communicate findings effectively.

Preferred Qualifications

• Experience with multiomic single-cell assays, including single-cell ATAC-seq, CITE-seq, immune profiling, cell hashing, feature barcoding, or spatial transcriptomics.
• Familiarity with downstream sequencing metrics and basic interpretation of single-cell data-quality outputs, such as read depth, mapping rates, sequencing saturation, genes detected per cell, UMI counts, mitochondrial read fraction, and doublet rates.
• Experience with laboratory automation or liquid-handling platforms.
• Familiarity with GxP, regulated documentation practices, or biomarker/translational research environments.

Working Environment:

This position is laboratory based and requires regular hands-on work with biological specimens, molecular biology reagents, and laboratory instrumentation. The role may require occasional flexibility to support time-sensitive sample processing and experimental schedules.

Contract lengths: 12 months with the chance to extend.

Pay Range

$40/hr-$44/hr.

Shift/Hours

Monday - Friday, occasional weekend work required.

Requisition Disclaimer

This job posting is for a temporary role with a third-party agency partner on assignment at Vertex Pharmaceuticals (“Vertex”). The individual selected for this role will be offered the role as an employee of a third- party agency partner; compensation, medical benefits, fringe benefits and other terms and conditions of employment shall be presented by the third-party agency partner upon offer. The pay rate range provided is a reasonable estimate of the anticipated compensation range for this job at the time of posting. The actual pay rate will be based on a number of factors, including skills, competencies, experience, location and/or being pursued and other job-related factors permitted by law. In addition, this role will be eligible for overtime pay, in accordance with federal and state requirements