10x Genomics - Monthly Newsletter (July)

10x_logo_vertical_full-color_digital.pngWelcome to our monthly 10x Genomics update!

Digital Events - July

Uncovering the Hidden Complexities of Plant Biology

Date: Wednesday 29th July 2020
Time: 3pm AEST

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Product Spotlight

The Visium Spatial Gene Expression Solution measures total mRNA in intact tissue sections and maps where gene activity is occurring. Immunostaining tissue sections with fluorescent antibodies enables simultaneous protein detection. Successful gene expression and protein visualisation is highly dependent on good imaging practices. 10X Genomics supports the use of the BioTek Cytation 7 imaging system

Download Visium Spatial Gene Expression Imaging Guidelines

Product Updates

NEW: Dual Indexing

Chromium Single Cell Gene Expression Solution now enables generation of dual index libraries to study gene expression profiles, cell surface protein expression, and/or CRISPR screening in hundreds to thousands of cells. Dual index libraries align with the industry standard for library configuration. Dual index libraries also increase confidence in assigned sample reads by mitigating index hopping effects with two unique sample indexes.

Check the resources here:

NEW: Chromium Single Cell Immune Profiling V2

The Chromium Single Cell Immune Profiling Solution provides a comprehensive approach to simultaneously examine cellular heterogeneity of the immune system, T and B cell repertoire diversity, and antigen specificity at single cell resolution. Single Cell Immune Profiling v2 vastly increases sensitivity, enabling detection of rare cell populations and phenotypes. Comprehensive immunophenotyping with this scale and resolution has never been more accessible.

Check out the resources for this new product here:

Targeted Gene Expression

Shipment of targeted gene expression products has commenced. The new targeted gene expression workflow is here. Compatible with 3', 5' and Visium libraries, you can now focus on the genes that matter most and reduce your sequencing by up to 90%!

Check out the resources here:

NEW Visium with Immunofluorescence

We are excited to officially launch the capability to run immunofluorescence with Visium!  Now customers can spatially detect protein and whole transcriptome gene expression simultaneously. The demonstrated protocol (DP) and updated software (Space Ranger v1.1 and Loupe Browser software v4.1) are available from our support page.

Check out the resources here:

NEW Visium Demonstrated Protocol

This protocol outlines the steps necessary to reset Visium Spatial slides containing incorrectly placed tissue for reuse with 10x Genomics Visium Spatial protocols. This protocol is compatible with both Visium Spatial Tissue Optimization and Visium Spatial Gene Expression slides. Slides must be reset prior to tissue permeabilization; once permeabilization has been started, slides can no longer be reused.

Check out the resources here:

Product Obsolescence Notification - Reminder

Don't forget the following non-NextGEM products will be dicointinuing soon. Plan to implement the NextGEM products now!

The Product Obsolescence Notification is available, summarizing:

  • Single Cell Gene Expression v3 (legacy GEM) - Dec 31, 2020
  • Single Cell Immune Profiling v1 (legacy GEM) - Dec 31, 2020
  • Single Cell ATAC v1 (legacy GEM) - June 30, 2020

Frequently Asked Questions

paul.jpg Hello and welcome to the 10x Newsletter.
My name is Paul Gooding and I'm the Field Application Scientist with Millennium Science for their Genomics portfolios in Australia and New Zealand.
I thought it would be fun to host an FAQ section where I could post the most common questions that I get asked about 10x Genomics solutions and technologies, and the most up to date responses. There is also a link to send in your own question, I will do my best to answer it in the following newsletter

What is the Minimum and Maximum Number of Cells that Can be Profiled for Single Cell Assays?

The Single Cell Gene Expression and VDJ assays are designed to target between 500 and 10,000 cells per sample. In cases where the sample is limiting, the following guidelines should be followed:

  • If possible, concentrate cells to achieve a cell stock concentration of ~700-1200 cells/µl
  • If concentrating the cells is not an option, load the cell suspension volume to the RT master mix without the addition of water to maximize cell count
  • In order to optimise the target cell count, extra care should be taken when assessing cell viability (>90% healthy) and cell aggregation under the microscope
  • Depending on your cell type of interest you may have very little cDNA going into the library prep. We support a wide range of total RNA and can use as little as 2 ng cDNA for library prep. If needed, the number of PCR cycles during cDNA amplification can be increased by 1-2 cycles to increase cDNA yield

Check out the below resources!

Using more than 10,000 cells per library increases the likelihood of the sample clogging the microfluidic channels in the chip. Each chip can process eight libraries in parallel (80,000 cells per chip).

Using too many cells also increases the multiplet rate, or the chance that you have more than one cell per GEM.

Have a question for Paul? Submit your question here

1,000 Publications!

1000-publications.jpegWe are happy to share that 10x Genomics hit 1,000 publications using 10x technologies!

Search the Publication Database

Visium Clinical Translation Research Networ (CTRN) Announcement

10x recently selected its first member of the Clinical Translational Research Network. We congratulate Joseph Powell and Alex Swarbrick of Garvan Institute and Arutha Kulasinghe of Queensland University of Technology who were successful in their applications!

Subscribe to the 10x Monthly Newsletter by Millennium Science here

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