Mar 26, 2025

Public workspace10x Protocols: Chromium GEM-X Single Cell 5' (CG000733|Rev A)  -- University of Minnesota TMCs

DOI
https://dx.doi.org/10.17504/protocols.io.bp2l6844dgqe/v1
  • Mythili Dileepan1,
  • 10X Genomics2,
  • Laura J Niedernhofer3,
  • Paul Robbins3
  • 1University of Minnesota;
  • 210X Genomics;
  • 3University of Minnesota, Minneapolis, MN
  • Cellular Senescence Network (SenNet) Method Development Community
Allie Abdellatif
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DOI: https://dx.doi.org/10.17504/protocols.io.bp2l6844dgqe/v1
Protocol Citation: Mythili Dileepan, 10X Genomics, Laura J Niedernhofer, Paul Robbins 2025. 10x Protocols: Chromium GEM-X Single Cell 5' (CG000733|Rev A) -- University of Minnesota TMCs. protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l6844dgqe/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 25, 2025
Last Modified: March 26, 2025
Protocol Integer ID: 125024
Keywords: nuclei from human adipose tissue, isolated nuclei, human adipose tissue, chromium gem, university of minnesota genomics center, minnesota genomics center, nuclei, cdna production, next gem technology, nuclei qc
Funders Acknowledgements:
NIH
Grant ID: 5U54AG076041
NIH
Grant ID: 5U54AG079754
Abstract
The nuclei from human adipose tissue were isolated using a protocol adapted from
three published articles. The isolated nuclei, kept on ice, were submitted to the
University of Minnesota Genomics Center (UMGC) for nuclei QC, cDNA production, and
library preparation. GEM-X uses the same Chromium scRNA-seq workflow but with
optimized reagents and improved microfluidics to enable increased sensitivity, higher
throughput, and improved sample recovery compared to the Next GEM technology.


Troubleshooting
Preparation
Complete single cell or nuclei isolation and 10x fixation prior to starting this protocol
Library Preparation
Download CG000733_ChromiumGEM-X_SingleCell5_ReagentKitsv3_UserGuide_RevA.pdfCG000733_ChromiumGEM-X_SingleCell5_ReagentKitsv3_UserGuide_RevA.pdf19.7MB

FASTQ Generation
BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq version 2.20.0