A Spatial and Temporal Transcriptomic Atlas of Mouse Intestinal Regeneration in the Jejunum

Description

Series information

Below we provide information on the replicates and accessing the data.

For intuitive or quicker analyses, you can use the Loupe Browser from 10x Genomics:

The following link can be used to access a download center for Loupe Browser or LoupeR packages, system requirements, and tutorials. https://www.10xgenomics.com/support/software/loupe-browser/latest

1. Download the latest version of Loupe Browser found on 10X Genomics website. There is a version for Windows or MacOS. You can use the link below.https://www.10xgenomics.com/support/software/loupe-browser/downloads

2. Download the dataset (8 µm bin resolution or cell segmentation, cloupe.cloupe file) from GEO GSE303705 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE303705).

3. To separate each slide by irradiation timepoint, the bins corresponding to each treatment are listed in .csv files located under "Spatial replicate metadatafiles" which can be uploaded to the Loupe Browser by selecting the Upload icon along the bottom left, to the right of "Create a New Group".

4. The link below provides a comprehensive walkthrough of most of the features and analysis tools of the Loupe Browser for the dataset.https://www.10xgenomics.com/support/software/loupe-browser/latest/tutorials/introduction/lb-navigation-for-spatial

5. The link below provides a slightly more in-depth description on analysis using unsupervised clustering, mapping “features” (genes of interest) on the image, mapping specific cell types, filtering barcodes, running DGE, and using the co-expression feature. https://www.10xgenomics.com/support/software/loupe-browser/latest/tutorials/assay-analysis/lb-hd-spatial-gene-expression

Briefly, you can switch visualization between the spatial tissue and bins or the UMAP generated by Space Ranger by selecting "Projection Type" along the top.

The projection visualization settings can be altered along the top, with changes for spot and tissue visual settings.

Across the bottom of the screen is differential expression results between the selected clusters, which can be selectively run by choosing different clusters or manually defined groups along the left.

With "Clusters" selected along the left, you can select between the Space Ranger generated Graph-based or K-means (2-10) clusters to visualize on the tissue.

"Features" allows for different visualizations of select genes or gene lists, which can be manually entered or uploaded from a csv file along the bottom left. Co-expression within "Features" or "Advanced Selection" along the left can be used to select bins with certain expression levels of specified genes.

"Reanalyze" along the left allows for subclustering of the selected clusters or groups.

Technical info (English)

Images and details of the replicates are below:

1. Rep1 dataset description: the dataset contains 4 time points post-irradiation (IR); 2 replicas of day 0 (non-IR control), and day 1, 3, and 5 post-IR. The tissues are arranged in a “rainbow” orientation. A labeled image is below.

2. Rep2 dataset description: the dataset contains 5 timepoints post-irradiation (IR); day 0 (non-IR control), and day 1, 2, 3, and 5 post-IR. The tissues are arranged in a “rainbow” orientation. A labeled image is below.

3. Rep3 dataset description: the dataset contains 4 timepoints post-irradiation (IR); day 0 (non-IR control), and day 1, 3, and 5 post-IR. The tissues are arranged in a “rainbow” orientation. A labeled image is below.

4. Rep4 dataset description: the dataset contains 4 timepoints post-irradiation (IR); day 0 (non-IR control), and 2 replicas of day 2, 2 replicas of day 4, and day 6 post-IR. The tissues are arranged in a “rainbow” orientation. A labeled image is below.