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
  • Mouse Brain

C5aR1 antagonism suppresses inflammatory glial gene expression and alters cellular signaling in an aggressive Alzheimer’s model

Nicole D Schartz, Heidi Y Liang, Klebea Carvalho, Shu-Hui Chu, Adrian Mendoza-Arvilla, Tiffany J Petrisko, Angela Gomez-Arboledas, Ali Mortazavi, Andrea Tenner

Inhibition of the C5aR1 receptor with PMX205 reduces plaque load and gliosis while improving short-term memory in Alzheimer’s Disease (AD) mouse models. Using scRNA-Seq and snRNA-Seq, the authors found that PMX205 treatment enhanced cell growth and repair and decreased the inflammatory gene expression in microglia despite little alteration of the protein levels in reactive cells. The results highlight the attractiveness of a C5aR1 inhibition-based strategy.

  • WT
  • Mouse Brain Nuclei

Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s Disease

Emily Miyoshi, Samuel Morabito, Caden M. Henningfield, Negin Rahimzadeh, Sepideh Kiani Shabestari, Sudeshna Das, Neethu Michael, Fairlie Reese, Zechuan Shi, Zhenkun Cao, Vanessa Scarfone, Miguel A. Arreola, Jackie Lu, Sierra Wright, Justine Silva, Kelsey Leavy, Ira T. Lott, Eric Doran, William H. Yong, Saba Shahin, Mari Perez-Rosendahl, Elizabeth Head, Kim N. Green, Vivek Swarup

Researchers used snRNA-Seq to compare gene expression in early and late-stage Alzheimer’s Disease (AD) and AD in Down Syndrome (DS), bridging the gap between genetic mouse models and sporadic AD. The study revealed a complex interaction between the extra chr21 and the genome, identified shared and unique pathways between late-stage AD and AD in DS, and discovered sex-related expression differences in AD in DS, enhancing our understanding of factors influencing AD progression.

  • WT
  • Organoids

Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture

Madison R Glass, Elisa A. Waxman, Satoshi Yamashita, Michael Lafferty, Alvaro Beltran, Tala Farah, Niyanta K Patel, Nana Matoba, Sara Ahmed, Mary Srivastava, Emma Drake, Liam T. Davis, Meghana Yeturi, Kexin Sun, Michael I. Love, Kazue Hashimoto-Torii, Deborah L. French, Jason L. Stein

In a multisite study to test the reproducibility of human cortical organoids (hCO) differentiation protocols, scRNA-Seq was used to characterize cross-site similarities and differences. The results showed reproducible key features, such as cell type proportions and structure, including neuroepithelial budding and cortical wall-like organization, as well as some differences that limit the utility of hCO models. Understanding how stem cell states influence early hCO cell types could lead to more reliable hCO protocols for studying neurodevelopmental disorders.

  • WT
  • Chicken Embryo

Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology

Jared A Tangeman, Sofia M Rebull, Erika Grajales-Esquivel, Jacob M Weaver, Stacy Bendezu-Sayas, Michael L Robinson, Salil A Lachke, Katia Del Rio-Tsonis

Using snRNA-Seq on chicken embryos, researchers profiled gene expression and chromatin accessibility associated with the chicken ocular lens development. They found three distinct populations representing major cell states (epithelial, intermediate, and fiber cell) and established a continuous trajectory from epithelial to fiber cell differentiation. The study confirmed known pathways and cataract-linked genes while uncovering new factors involved in lens development, homeostasis, and pathology.

  • WT
  • PBMCs

Comparative analysis of single-cell RNA sequencing methods with and without sample multiplexing

Yi Xie, Huimei Chen, Vasuki Ranjani Chellamuthu, Ahmad bin Mohamed Lajam, Salvatore Albani, Andrea Hsiu Ling Low, Enrico Petretto, Jacques Behmoaras

Parse and 10X were compared using scRNA-seq on PBMC from 2 healthy donors. Parse demonstrated better data quality with lower multiplets rates but had lower cell recovery. Parse detected 1.2-fold more genes, had better clustering performance, and greater power in distinguishing cell types with specific gene signatures. Parse also excelled in detecting longer transcripts and rare cell types.

  • WT Mega
  • Lung

Epithelial Yap/Taz are required for functional alveolar regeneration following acute lung injury

Gianluca T. DiGiovanni, Wei Han, Taylor Sherrill, Chase J. Taylor, David S. Nichols, Natalie M. Geis, Ujjal K. Singha, Carla L. Calvi, A. Scott McCall, Molly M. Dixon, Yang Lui, Ji-Hoon Jang, Sergey S. Gutor, Vasiliy V. Polosukhin, Timothy S. Blackwell, Jonathan A. Kropski, Jason J. Gokey

Alveolar epithelium regeneration and repair following injury is not completely understood. Evidence suggests that the Hippo-YAP/TAZ pathway is vital for AT2 to AT1 development and dysregulation of this pathway is a key feature of idiopathic pulmonary fibrosis. In a mouse model, AT2 cells lacking YAP/TAZ were injured with bleomycin. scRNA-Seq showed upregulated fibroblast activation markers, increased fibrillar collagen expression, and prolonged inflammation 28 days post-injury, ultimately resulting in lung fibrosis.

  • WT Mini
  • Mouse Nuclei

Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis

Carina Shiau, Jingyi Cao, Mark T Gregory, Dennis Gong, Xunqin Yin, Jae-Won Cho, Peter L Wang, Jennifer Su, Steven Wang, Jason W Reeves, Tae Kyung Kim, Youngmi Kim, Jimmy A Guo, Nicole A Lester, Nathan Schurman, Jamie L Barth, Ralph Weissleder, Tyler Jacks, Motaz Qadan, Theodore S Hong, Jennifer Y Wo, Hannah Roberts, Joseph M Beechem, Carlos Fernandez-del Castillo, Mari Mino-Kenudson, David T Ting, Martin Hemberg, William L Hwang

Spatial molecular imaging is combined with single-cell sequencing to characterize the tumor microenvironment of human pancreatic cancer. These multi-modal data lead to the generation of the SCOTIA model to better explain the emergence of treatment resistance.

  • WT
  • MB Organoids

Preventing recurrence in Sonic Hedgehog Subgroup Medulloblastoma using OLIG2 inhibitor CT-179

Yuchen Li, Chaemin Lim, Taylor Dismuke, Daniel Malawsky, Sho Oasa, Zara Bruce, Carolin Offenhäuser, Ulrich Baumgartner, Rochele D'Souza, Stacey Edwards, Juliet French, Lucy Ock, Sneha Nair, Haran Sivakumaran, Lachlan Harris, Andrey Tikunov, Duhyeong Hwang, Coral Del Mar Alicea Pauneto, Mellissa Maybury, Timothy Hassall, Brandon Wainwright, Santosh Kesari, Gregory Stein, Michael Piper, Terrance Johns, Marina Sokolsky-Papkov, Lars Terenius, Vladana Vukojevic, Bryan Day, Timothy Gershon

Using an organoid and mouse model of SHH medulloblastoma (MB), scRNA-seq data shows tumor cells expressing the reoccurrence driver OLIG2, are disrupted by CT-179 with minimal off-target toxicity. Post-treatment, tumors up-regulate CDK4 mediating CT-179 resistance. However, combined therapy with a CDK4/6 inhibitor delayed cancer recurrence compared to either single agent.

  • WT
  • Human Organoids

Generating human neural diversity with a multiplexed morphogen screen in organoids

Neal D. Amin, Kevin W. Kelley, Jin Hao, Yuki Miura, Genta Narazaki, Tommy Li, Patrick McQueen, Shravanti Kulkarni, Sergey Pavlov, Sergiu P. Paşca

Using scRNA-seq, researchers developed a scalable screening platform to establish a morphogen atlas of human neural cell fate. By applying 14 morphogen modulators to neural organoids, they identified distinct cellular and structural characteristics of brain regions and critical timing windows.

  • WT Mega
  • Human PBMCs

Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases

Yoshiaki Yasumizu, Daiki Takeuchi, Reo Morimoto, Yusuke Takeshima, Tatsusada Okuno, Makoto Kinoshita, Takayoshi Morita, Yasuhiro Kato, Min Wang, Daisuke Motooka, Daisuke Okuzaki, Yamami Nakamura, Norihisa Mikami, Masaya Arai, Xuan Zhang, Atsushi Kumanogoh, Hideki Mochizuki, Naganari Ohkura, Shimon Sakaguchi

Using scRNA-seq data of CD4+ T cells from healthy individuals and autoimmune disease patients, clustering was performed through non-negative matrix factorization (NMF). Analysis of publicly available scRNA-seq datasets identified 12 transcriptional gene programs that characterized each autoimmune disease and predicted clinical status accurately.