Lumbar DRG neurons from adult mice fed on a regular diet (n = 5 animals) and a high-fat diet (n = 5 animals) were isolated and dissociated following protocol established by Zeisel et al., 2018. A high viability single-cell suspension was prepared, and using the 10X Genomics chromium single cell kit v2, about 6000-8000 cells were recovered. Two rounds of the experiment (total n = 10 animals per group) were performed, and downstream cDNA synthesis, library preparation, and sequencing were performed according to the manufacturer's instruction. Illumina runs were demultiplexed and aligned using the 10X Genomics cell ranger pipeline. Dimensionality reduction, clustering, and differential expression of genes were done in Seurat v4.2.35 (link) Raw matrix files for single-cell RNA sequencing were deposited in Dryad (https://doi.org/10.5061/dryad.9s4mw6mm5 ).
Genomics cell ranger pipeline
Manufactured by 10x Genomics
The 10X Genomics cell ranger pipeline is a bioinformatics software suite that processes and analyzes single-cell RNA sequencing data. It is designed to handle the complex data generated by 10X Genomics' single-cell sequencing platforms, performing tasks such as read alignment, cell barcode identification, and gene expression quantification.
Automatically generated - may contain errors
2 protocols using genomics cell ranger pipeline
1
Single-Cell Transcriptomics of Mouse Lumbar DRG Neurons
2
Single-Cell RNA-Seq Analysis of HNSCC Tumors
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To obtain cells for scRNA‐seq analysis, the HNSCC tumors were dissociated using a tumor dissociation kit (Miltenyi Biotec), and dead cells were removed using a dead cell removal kit (MACS). Single cell suspension from tumors with viability greater than 80% was loaded onto the 10x Genomics Next GEM Chip G for the target capture of ≈8000 cells/chip. For library construction and sequencing, droplet‐based scRNA‐seq (10x Genomics Chromium Single Cell 3’ Reagent Kit v3.1 no. 1000121) was used for single‐cell library preparation. After reverse transcription, cDNA sequencing was performed using the Illumina Novaseq 6000 (Illumina, Inc.). scRNA‐seq reads were processed using a 10x Genomics Cell Ranger pipeline (version 6.1.1, 10x Genomics). Chemistry Batch Correction algorithm (Cell Ranger v3) was used to correct batch effects between samples. The algorithm is based on mutual nearest neighbors (MNN) to identify similar cell subpopulation between batches. Then data were analyzed by 10× Loupe Browser (version 6.2, 10x Genomics). The clustering of cells in the dataset was performed using a Uniform Manifold Approximation and Projection (UMAP) algorithm in Loupe Browser. GO analysis of differentially expressed genes between clusters was performed using the online Enricher website (https://maayanlab.cloud/Enrichr/ ).
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