diff --git a/index.html b/index.html new file mode 100644 index 00000000..ae5b1840 --- /dev/null +++ b/index.html @@ -0,0 +1,574 @@ + + + + + + + + + + + + + +Integration of single-nucleus and spatial transcriptomics reveals the molecular landscape of the human hippocampus + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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This is the repository for the spatial (U01) hippocampus (HPC) +project. The README.md contains a description of files in the repository +including code and data to analyze the HPC data.

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Study design

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Experimental design to generate paired single-nucleus RNA-sequencing +(snRNA-seq) and spatially-resolved transcriptomics (SRT) data in the +human hippocampus. (A) Postmortem human tissue blocks from the anterior +hippocampus were dissected from 10 adult neurotypical brain donors. +Tissue blocks were scored and cryosectioned for snRNA-seq assays (red), +and placement on Visium slides (Visium H&E, black; Visium Spatial +Proteogenomics (SPG), yellow). (B) 10μm tissue sections from all ten +donors were placed onto 2-5 capture areas to include the extent of the +HPC(n=36 total capture areas), for measurement with the 10x Genomics +Visium H&E platform. (C) 10μm tissue sections from two donors were +placed onto 4 capture areas (n=8 total capture areas) for measurement +with the 10x Genomics Visium-SPG platform. (D) Tissue sections (2-4 +100μm cryosections per assay) from all ten donors were collected from +the same tissue blocks for measurement with the 10x Genomics 3’ gene +expression platform . For each donor, we sorted on both and PI+NeuN+ +(n=26 total snRNA-seq libraries).

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Description of HPC data

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This is a description of data files for this project.

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  1. The MiSeq and NovaSeq folders has +softlinks to the fastqs of slides V10B01−085 and +V10B01−086
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  2. The 2022-04-12_SPag033122 folder has softlinks to the +fastqs of slides V11A20−297, V11L05−333, +V11L05−335, V11L05−336, +V11U08−081, V11U08−084.
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Description of analyses of HPC data

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REDCap

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  • Script to extract HPC info only from the redcap form and extract all +relevant (demographic/biological/rotation info etc) data to add to the +spe object is here
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01_spaceranger

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Code to align reads using 10x SpaceRanger - Script to run space +ranger with miseq and novaseq fastqs combined for samples +V10B01−085 and V10B01−086 is here. +- Script to run space ranger for all other samples is here.

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02_build_spe

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Code to build initial SPE, rotate/rearrange capture areas to better +reflect anatomy, and drop spots - Script to build initial raw +SpatialExperiment (SPE) object from spaceranger output is 01_raw_spe_allSamples.R. +- Script to perform rotations and rearrange capture areas is 02_transform_spe_allSamples.R +- Script to remove drop spots not in tissue section and spots with zero +counts is 03_dropSpots.R.

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03_shiny app_basic

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Code to build temporary R Shiny app for initial manual annotations - +Script to subset the basic_spe to make it memory effecient for shiny app +is here. +- Script to deploy the shiny app is here. +- Scripts for running the shiny app is here.

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04_QC

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Code to perform QC on SRT data - Script to run QC is here +- Script to plot results from QC is here

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05_preprocess_batchCorrection

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Code to preprocess data for clustering is here

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06_clustering

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Code to cluster SRT data. Primary method for clustering was PRECAST. +Code for formatting data, running PRECAST, and visualizing results is here.

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08_pseudobulk

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Code to perform pseudobulk DE analysis is here

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nnSVG

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Code to identify spatially variable genes (SVGs) is here

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spot_deconvo

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Code for running spot-level deconvolution is here

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NMF

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Code to project NMF patterns learned in paired snRNA-seq data to +Visium data and visualize results is here

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enrichment_analysis

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Code for running LDSC across spatial domains, snRNA-seq cell classes, +and NMF patterns is here

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Cell segmentation

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VistoSeg here

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cellpose here

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