Spatial and Single-Nuclei Transcriptomics of Plant-Fungus Symbiosis

Cellranger and Spaceranger software (10x Genomics) were used to preprocess single-nuclei and spatial transcriptomic sequencing libraries, respectively. A formatted reference genome was generated using Cellranger or Spaceranger’s ‘mkref’ function using the Medicago truncatula MedtrA17_4.0 (ref. ^{37 (link)}) whole genome sequence and annotation and the Rhizophagus irregularis Rir_HGAP_ii_V2 (DAOM 181602, DAOM 197198)^{38 (link)} whole genome sequence and annotation using default parameters. Single-nuclei and spatial reads were aligned to the genome references using the ‘count’ function in Cellranger 7.0 and Spaceranger 1.3 software packages (10x Genomics), respectively. Brightfield tissue images were aligned to the spatial capture area fiducial frame and voxels corresponding to overlaying tissue were manually selected for all capture areas in Loupe Browser (10x Genomics). Data analysis for both the single-nuclei and spatial data was performed using the Seurat^{22 (link)} 4.3.0 package in R 4.2.1 available at https://www.R-project.org.

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Serrano K., Bezrutczyk M., Goudeau D., Dao T., O’Malley R., Malmstrom R.R., Visel A., Scheller H.V, & Cole B. (2024). Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis. Nature Plants, 10(4), 673-688.

Publication 2024

Spaceranger Loupe Browser

Corresponding Organization :

Other organizations : Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Joint Genome Institute

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Variable analysis

independent variables

Use of Cellranger and Spaceranger software (10x Genomics) to preprocess single-nuclei and spatial transcriptomic sequencing libraries, respectively

dependent variables

Transcriptomic profiles from single-nuclei and spatial transcriptomic sequencing libraries

control variables

Use of the Medicago truncatula MedtrA17_4.0 (ref. ^{37 (link)}) whole genome sequence and annotation and the Rhizophagus irregularis Rir_HGAP_ii_V2 (DAOM 181602, DAOM 197198)^{38 (link)} whole genome sequence and annotation as the reference genomes
Use of default parameters for generating the formatted reference genomes
Alignment of single-nuclei and spatial reads to the genome references using the 'count' function in Cellranger 7.0 and Spaceranger 1.3 software packages (10x Genomics), respectively
Manual selection of voxels corresponding to overlaying tissue for all capture areas in Loupe Browser (10x Genomics)
Use of the Seurat 4.3.0 package in R 4.2.1 for data analysis of both the single-nuclei and spatial data

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