Welcome to the 10x Blog

From tips and tricks to 10x news, our blog is here to help you learn about all things 10x. Let us know what topics you would like to see in the Community Suggestions forum.

Single-cell RNA-seq enables researchers to examine gene expression on a cell-by-cell basis providing insights into the function and regulation of complex biological systems.  In our recent 10x-pert Workshop, R&D scientists discussed single-cell RNA-seq data analysis tools, including Cell Ranger™ analysis pipelines, and performed a live demo of Loupe™ Cell Browser for data visualization.
A recent PNAS publication from the laboratory of Dennis Lo applied the use of the 10x Genomics’ Chromium™ Single Cell 3’ Solution to comprehensively characterize the transcriptomic heterogeneity of the human placenta—an approach that served as confirmation for the non-invasive identification of cellular dysfunction during gestational complications such as preeclampsia.
Linked-Reads provide long-range information enabling structural variant detection and phasing of genome and exome sequencing data.  In our third 10x-pert Workshop session, our R&D 10x-perts provided an overview of the Loupe™ Genome Browser for structural variant detection and took closer look at visualizing simple structural variants and deriving complex events.
High quality high molecular weight (HMW) DNA is key to getting the most out of Linked-Read data. In a recent 10x-pert Workshop session, our R&D 10x-pert discussed general tips and best practices for isolating HMW DNA and took a closer look at two of our demonstrated protocols for HMW DNA isolation from fresh frozen tissues and DNA size selection.
We recently hosted our first live, online 10x-pert Workshop featuring single-cell sample prep topics.  Two of our R&D scientists gave a presentation detailing general do’s and don’ts followed by a closer look at two of our demonstrated protocols for preparing nuclei for single-cell RNA-seq and removing dead cells.
Have you ever wondered how to best prepare your samples or how much sequencing you need to achieve the highest quality Linked-Read data? We recently published a Bench Tips article with Biocompare, where we highlight important tips to make the most of our Linked-Read technology for long-range genomic analysis.
Transcriptome analysis has made the leap from bulk population-based studies to the single cell, and scientists are harnessing this new degree of resolution with remarkable ingenuity.  By analyzing the transcriptome of a single cell at a time, the heterogeneity of a sample is captured and resolved to the fundamental unit of living organisms—the cell.
In a new Cell Stem Cell publication, Yan et al, demonstrate the utility of single cell RNA-seq to study intestinal stem cell heterogeneity, lineage hierarchy and identify potential new stem cell markers.
Researchers at Stanford University have developed novel bioinformatics tools that leverage 10x Genomics’ Linked-Read sequencing to phase and resolve the complete structure of cancer genomic rearrangements. 
The introduction of single cell technologies has provided researchers the tools to dissect and understand biological systems like never before.  Insights into the burgeoning single-cell field has recently been the focus of a special issue in Nature.
Two recent publications applied the power of Linked-Reads and the Chromium™ Genome Solution to genetically characterize gastric and triple-negative breast cancer. In both cases, the researchers discovered complex genomic rearrangements that they associated with the amplification of oncogenic driver genes.
New to 10x or need a refresher?  No problem.  Check out our new Chromium™ Single Cell 3’ training video series. Learn more about GemCode™ technology, single cell sample prep, data analysis and more.
Get the most out of your Linked-Read data with Long Ranger™ version 2.1.4: improved run-times, extended support for NovaSeq and more.
In a new scientific seminar video, Dr. Britt Adamson, a Postdoctoral Fellow from the Weissman Lab at UCSF, presents her work using a novel method, Perturb-seq, to dissect the dynamic transcriptional mechanisms of the unfolded protein response.
In our June 22nd Nature Webcast, Dr. Aude Chapuis, who was recently awarded initial funding in a competition to develop projects that utilize single-cell RNA sequencing to improve research into immunotherapy-based cancer treatment, presented her T-cell immunotherapy research, highlighting the applications of scRNA-seq in developing new T-cell therapy approaches.
In a recent article in GEN, Brian Fritz, Ph.D. describes how the Chromium™ Single Cell V(D)J Solution reveals true T-cell diversity by combining microfluidics and 5' molecular barcoding to assemble full-length V(D)J sequences on a cell-by-cell basis.
A collaborative research study with Stanford University School of Medicine researchers was recently published in Nature. The article, “Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem-cell self-renewal,” describes how the 10x Genomics’ Single Cell 3’ Solution for single-cell RNA-seq (scRNA-seq) was utilized to help unravel the priming and self-renewal mechanisms of intestinal stem cells (ISCs).     
Using single-cell sequencing and a battery of molecular tools, the authors achieved unprecedented insight into epithelial cell lineage relationships and the dynamics of differentiation in murine lacrimal gland development.
The International Society for Stem Cell Research (ISSCR) annual meeting brings together stem cell researchers from around the world to share their work, discuss tools and techniques, and advance stem cell science and regenerative medicine.  Join us for our Innovation Showcase on Friday June 16 featuring 10x's Tarjei Mikkelsen and featured guest speaker, Julie Sneddon, Assitant Professor, UCSF School of Medicine.
There are many examples of how microbes influence the behavior of animals; however, studying the molecular basis for microbial behavior manipulation has suffered from a lack of tools. At our Bay Area User Group Meeting, Carolyn Elya spoke about establishing a D. melanogaster – E. muscae system and setting out to sequence and assemble the mind-controlling fungal pathogen.
Using 10x Linked-Read technology combined with standard, short-read sequencing, Dr. Noah Spies and his team at Stanford University were able to develop a statistical method for complex structural variant detection—Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs).
The Supernova™ Assembler enables true diploid assembly from Linked-Reads and the latest release makes everyday de novo assembly more accessible than ever.
Profile full-length paired V(D)J transcripts from hundreds to millions of lymphocytes with the new Chromium™ Single Cell V(D)J Software Suite – part of the Chromium™ Single Cell V(D)J Solution.
Seattle Children’s announces the first clinical trial applying next-generation T-cell receptor (TCR) sequencing and single-cell gene expression analysis to better understand the role of the immune system in inflammatory bowel disease and graft-versus host disease in pediatric patients.
We'll be at ESHG 2017 in Copenhagen! Join us for our Corporate Satellite on Monday, May 29th to hear more about the Chromium System, 10x Software Solutions and more.
There’s a growing number of data analysis tools being developed for single cell and Linked-Read applications, including gene expression, genome assembly, structural variant detection and more.  Check out the list we’ve compiled so far.
Genomic analysis is an important tool for conservation biology, enabling researchers to help better understand and preserve endangered species. In a new Biorxiv preprint, researchers at Johns Hopkins describe a cost-effective and low DNA input method of de novo assembly for the endangered Hawaiian monk seal genome using 10x Linked-Reads and Supernova™ software.
Although thousands of human genomes have been sequenced in the last decade, de novo assembly of individual genomes is not common due to the high cost and experimental burden.  In a recent Genome Research paper, Weisenfeld et al describe a straightforward, low cost method for creating true diploid de novo assemblies using 10x Genomics Linked-Reads and the Supernova™ assembler.
Five scientists from Fred Hutchinson Cancer Research Center were awarded the initial stage of funding in a competition sponsored by the Immunotherapy Integrated Research Center to develop projects that utilize single-cell RNA sequencing and 10x Genomics technology.
The large scale and repetitive nature of conifer genomes make them an important benchmark for assembly technologies. At 31 Gb, the Pinus lambertiana (sugar pine) genome is the largest genome assembled to date. Using the GemCode™ System from 10x Genomics, researchers at UC Davis scaffolded the de novo assembly and produced a new reference assembly for sugar pine with 8-fold improvement in contiguity.