Company

Technology

Discover scalable, instrument-free single cell sequencing technology from Parse Bioscience

Technology Overview


Resources

Explore our collection of resources to learn more about technology and its applications from leading researchers

Resources Overview

Company

Providing researchers single cell sequencing with unprecedented scale and ease

About Parse

Technology

Discover scalable, instrument-free single cell sequencing technology from Parse Bioscience

Technology Overview

Publications and Posters

Parse has an ecosystem of products to help take your single cell research further. Delve deeper into the details here.

Publications

  • WT Mini
  • Bovine Tracheal Organoids

Development of Matrix-Embedded Bovine Tracheal Organoids to Study the Innate Immune Response against Bovine Respiratory Disease

Pin Shie Quah, Bang M. Tran, Vincent D.A. Corbin, Jessie J.-Y. Chang, Chinn Yi Wong, Andrés Diaz-Méndez, Carol A. Hartley, Weiguang Zeng, Eric Hanssen, Zlatan Trifunovic, Patrick C. Reading, David C. Jackson, Elizabeth Vincan, Lachlan J.M. Coin, Georgia Deliyannis

To enhance research into BHV-1, authors developed a 3-D matrix system for bovine tracheal organoid culture. scRNA-seq data showed vulnerability to BHV-1 virus and robust immune response to stimulation by Pam2Cys, demonstrating the utility of the 3-D model system in studying viral infections.

  • WT
  • Human MSCs

Mesenchymal stem cells ameliorate inflammation in an experimental model of Crohn’s disease via the mesentery

Maneesh Dave, Atul Dev, Rodrigo A Somoza, Nan Zhao, Satish Viswanath, Pooja Rani Mina, Prathyush Chirra, Verena Carola Obmann, Ganapati H Mahabeleshwar, Paola Menghini, Blythe Durbin Johnson, Jan A Nolta, Christopher Soto, Abdullah Osme, Lam T Khuat, William Murphy, Arnold I Caplan, Fabio Cominelli

Human Mesenchymal Stem Cells (hMSC) modulate T cells and macrophages when administered into a Chron’s disease model. scRNA-seq showed long-term anti-inflammatory macrophage reprogramming, providing evidence of prolonged therapeutic effects of hMSC.

  • WT Mini
  • Human Liver

Characterization of Pro-Fibrotic Signaling Pathways using Human Hepatic Organoids

Yuan Guan, Zhuoqing Fang, Angelina Hu, Sarah Roberts, Patrik K. Johansson, Sarah C. Heilshorn, Annika Enejder, Gary Peltz

In a hepatic organoid model, scRNA-seq identified the liver fibrosis-inducing ligand. TGFβ1 exposure transformed mesenchymal cells into myofibroblast-like cells, upregulating proteases, anti-proteases, and extracellular matrix genes, thereby promoting liver fibrosis development.

  • WT
  • PBMCs

High-quality functional association networks inferred from scRNA-seq and proteomics data

Mikaela Koutrouli, Pau Piera Líndez, Robbin Bouwmeester, Simon Rasmussen, Lennart Martens, Lars Juhl Jensen

Introduces FAVA, a novel analysis method to handle large-scale scRNA-seq and proteomic data, predict high-confidence functional associations, and provide good coverage for understudied proteins. Performance was evaluated using freely available proteomic and PBMC scRNA-Seq datasets.

  • WT Mini
  • Human IPS

Human iPS cell-derived sensory neurons can be infected by SARS-CoV-2 strain WA1/2020 as well as variants delta and omicron

Anthony Flamier, Punam Bisht, Alexsia Richards, Danielle Tomasello, Rudolf Jaenisch

In COVID-19-infected human sensory neurons, scRNA-seq was critical in revealing that sensory neurons can be infected by SARS-CoV-2 but are unable to produce new viruses. This may have implications for understanding the infection’s long-term impact on the peripheral nervous system.

  • WT
  • Zebrafish Retina

Notch Inhibition Promotes Regeneration and Immunosuppression Supports Cone Survival in a Zebrafish Model of Inherited Retinal Dystrophy

Joseph Fogerty, Ping Song, Patrick Boyd, Sarah E. Grabinski, Thanh Hoang, Adrian Reich, Lauren T. Cianciolo, Seth Blackshaw, Jeff S. Mumm, David R. Hyde, and Brian D. Perkins

In a zebrafish model of progressive retinal degeneration, inflammation alone was not sufficient to trigger Müller glia reprogramming into multipotent retinal progenitors. Single cell RNA-seq showed that notch signaling remained active with progressive degeneration in contrast to what has been seen previously with acute injury.

  • WT
  • Mouse Brain
  • +1

High sensitivity single cell RNA sequencing with split pool barcoding

Vuong Tran, Efthymia Papalexi, Sarah Schroeder, Grace Kim, Ajay Sapre, Joey Pangallo, Alex Sova, Peter Matulich, Lauren Kenyon, Zeynep Sayar, Ryan Koehler, Daniel Diaz, Archita Gadkari, Kamy Howitz, Maria Nigos, Charles M. Roco, and Alexander B. Rosenberg

A detailed performance evaluation of Evercode™ WT v2 that highlights improved gene and transcript detection, robustness across samples, and no bias in gene expression data. Multiple sample types were assessed, including cells and nuclei.

  • WT Mega
  • Human PBMCs

High dimensional co-expression networks enable discovery of transcriptomic drivers in complex biological systems

Samuel Morabito, Fairlie Reese, Negin Rahimzadeh, Emily Miyoshi, and Vivek Swarup

Introduces hdWGCNA, an analysis framework supporting system-level analysis of data from complex biological systems. Data was integrated from the 1M Evercode WT Mega v1 Type-1 Diabetes dataset from human PBMCs to demonstrate utility and scalability.
  • WT
  • Mouse Brain

Single-nuclei transcriptomics of mammalian prion diseases identifies dynamic gene signatures shared between species

Athanasios Dimitriadis, Fuquan Zhang, Thomas Murphy, Thomas Trainer, Zane Jaunmuktane, Christian Schmidt, Tamsin Nazari, Jacqueline Linehan, Sebastian Brandner, John Collinge, Simon Mead, and Emmanuelle Viré

Transcriptomic studies on prion-infected mouse brains revealed gene signatures similar to human prion disease, shedding light on underlying molecular mechanisms. By introducing a protein denaturation step, samples could be transferred from a BSL-3 to a BSL-2 lab for library preparation and sequencing.

  • WT Mega
  • Human IPSCs

Directed Differentiation of Human iPSCs to Functional Ovarian Granulosa-Like Cells via Transcription Factor Overexpression

Merrick Pierson Smela, Christian Kramme, Patrick Fortuna, Jessica Adams, Edward Dong, Mutsumi Kobayashi, Garyk Brixi, Emma Tysinger, Richie. E. Kohman, Toshi Shioda, Pranam Chatterjee, and George M. Church

Two transcription factors required for developing ovarian granulosa cells – previously lacking components of human ovary organoids – were identified. Human iPSCs were induced to differentiate into human ovary organoids, whose identities were confirmed based on differential gene expression.