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Cell Ranger


10x Genomics
Chromium Single Cell Immune Profiling

What is HT (High Throughput)?

The Chromium Next GEM Single Cell 5' HT kits (referred to as high throughput or HT) are high throughput, cost-effective solutions for profiling gene expression at the single cell level. In combination with Feature Barcode technology the 5' HT assays also enable simultaneous cell surface protein detection and CRISPR profiling in single cells. The HT kits offer 16 channels per chip, and allow more cells to be recovered per channel:

Chromium X Series

The Chromium X Series is the next generation of 10x Genomics instrumentation, purposefully designed to enable high-throughput experiments, offering a highly optimized approach to single cell studies. The Chromium X Series is one instrument, available in two firmware options (Chromium X and Chromium iX). All 10x Genomics single cell dual index assays are supported on Chromium X Series instruments, but the HT kits can only be run on the Chromium X, not iX.

Analyzing HT Data with Cell Ranger

Cell Ranger v6.1 or later is required to analyze HT data. After demultiplexing the BCL files with cellranger mkfastq, run cellranger count or cellranger multi on the FASTQ data to obtain output files.

The Chromium X enables million-cell experiments to be run on a single HT chip. To aggregate data from multiple GEM wells requires running cellranger aggr on the molecule_info.h5 files output by cellranger count or cellranger multi.

Cell Ranger processes HT libraries similarly to standard libraries except for minor adjustments to certain parameters in the cell calling algorithm. Starting with Cell Ranger 7.0, the expected number of cells can be auto-estimated or specified with --expect-cells (see Gene Expression algorithm overview).