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.

Researchers recently introduced a new software package for simulating Linked-Reads call LRSim. In a new paper by Luo et al., the authors demonstrate how the software can be used to optimize Linked-Read sequencing results.
The 2017 Australasian Genomic Technologies Association (AGTA) in Hobart, Tasmania wrapped up last week and a common theme of the meeting was both applications and technical challenges of single-cell analysis.
In a new publication in Nature, Broad Institute researchers utilized single-cell RNA-seq to identify and characterize novel small intestinal epithelial cell types and explore epithelial cell composition upon pathogen challenge and during homeostasis.
In a new Cell Reports article, researchers utilized single-cell RNA-seq to help identify and characterize a subset of triple negative breast cancer (TNBC) tumors associated with sensitivity to EGFR-inhibition.
In a recent Bioinformatics publication, researchers presented ARCS, a new application that uses 10x Linked-Reads to further organize draft genomes into highly contiguous assemblies.
The American Society of Human Genetics (ASHG) annual meeting continued in Orlando, FL and Thursday bought our 10x Software workshop "Intuitive Tools for Sequence Analysis: Crunching Genomic, Single-Cell, and Immune Repertoire Data Using 10x Chromium™ Software” and an exciting PerkinElmer workshop where they discussed "Linked-Reads: Enabling Robust Genome Analysis from Dried Blood Spots”.
The American Society of Human Genetics (ASHG) annual meeting started this week in Orlando, FL and there have been some exciting sessions, talks, posters and more.  We also had our first of two workshops featuring Hakon Hakonarson of CHOP and Madhuri Hedge of PerkinElmer.
The ASHG 2017 Presidential Symposium on Wednesday, October 18 featured speakers Bill Gates, Co-chair and Trustee of the Bill & Melinda Gates Foundation, and Francis Collins, Director of the U.S. National Institutes of Health, and was a lively conversation about global health and genomics.
The American Society of Human Genetics annual meeting took place from October 17 to 21 in Orlando, FL and we are excited to re-cap what 10x was up to including workshops, talks, posters and more.
Profiling paired V(D)J transcripts from hundreds to millions of lymphocytes on a cell-by-cell basis, the Chromium™ Single Cell V(D)J system is a complete, scalable tool that has the potential to accelerate progress in immune therapy development.  In our recent 10x-pert Workshop, R&D scientists discussed the V(D)J Solution and performed a live demo of Loupe™ V(D)J Browser for data visualization.
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.