Single cell RNA-seq analysis machine (May 2023 version) | Information dissemination media for research and development TEGAKARI

A customer inquired about the introduction of a PC for single-cell RNA-seq analysis.
Currently, I am using a Mac, and I am using Cell Ranger in a Linux environment built with Docker, but the problem is that it takes a long time to process.
In this consultation, we assume a Linux machine with a budget of about 60 yen, and the condition is that the memory is 128 GB or more as a spec.

Based on the information we received, we proposed the following configuration.

CPU	Core i9-13900KS (3.20GHz 8 cores + 2.40GHz 16 cores)
memory	128GB
Storage 1	2TB M.2 SSD
Storage 2	16TB HDD S-ATA
video	NVIDIA T400 4GB MiniDisplayPort x3
network	on board(2.5GBase-T x1) Wi-Fi x1
Housing + power supply	Tower type housing + 850W
OS	Ubuntu 22.04

Since you wanted a Linux machine, I proposed an Ubuntu machine within your budget.The memory is 128GB, and assuming the need for usage, it is configured with SSD + large capacity HDD. The recommended specs for Cell Ranger are 16 CPU cores + 128GB memory.The memory capacity of this configuration is the maximum according to the specifications, so please contact us if there is a possibility that more memory may be required.

The configuration of this case study is based on the conditions given by the customer.
Please feel free to contact us even if you are considering different conditions from what is posted.

■ Keywords

・What is single-cell RNA-seq?
Single-cell RNA-seq is a technology that enables analysis of gene expression at the level of individual cells.Cell-to-cell differences are revealed by performing transcriptome mapping of cells.Such an analysis method is required because even cells of the same type have minute individual differences.Applications include elucidation of heterogeneity within cancer cells and elucidation of the process of cell differentiation.In addition, it is possible to analyze from a small amount of RNA, and it is used for detailed analysis.

・What is Cell Ranger?
Cell Ranger is a software pipeline from 10x Genomics.Single-cell RNA-sequencing data can be processed, clustered, and gene expression quantified. Process single-cell RNA-seq data generated using 1x Genomics Chrome and perform gene expression clustering to identify single-cell subpopulations.In addition, it also supports creation of expression matrix by mapping to virtual reference and quantifying genes.