From 2cce8efef8c12880788aebc9b434c055993e4af8 Mon Sep 17 00:00:00 2001 From: Bernie Mulvey Date: Thu, 5 Dec 2024 11:58:45 -0600 Subject: [PATCH] Add files via upload --- index.html | 346 ++++++++++++++++++++++------------------------------- 1 file changed, 142 insertions(+), 204 deletions(-) diff --git a/index.html b/index.html index 21c6a1162..b2d0dc701 100644 --- a/index.html +++ b/index.html @@ -1,15 +1,17 @@ - - - - - + + + + + -index + + +Integration of single-nucleus and spatial transcriptomics reveals the molecular landscape of the human hippocampus - + + - - + + +
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Integration of single-nucleus and spatial +transcriptomics reveals the molecular landscape of the human +hippocampus

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Spatially-resolved molecular sex differences at single cell -resolution in the adult human hypothalamus

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DOI PENDING

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Study Design

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The hypothalamus is a critical brain area underlying functions with -inherent sex differences, such as reproductive physiology, endocrine -signaling, and metabolism. In the rodent, these sex-differentiated -functions correspond to differences in volume, cell type composition, -and gene expression between males and females across individual -hypothalamic regions (here, “domains”). The ventromedial hypothalamus -(VMH) and arcuate nucleus (ARC) are two hypothalamic regions that -influence appetitive/social behaviors and growth/metabolism, -respectively. While molecular profiling studies in the rodent -hypothalamus have identified specialized cell types with unique -transcriptomic signatures, there is a paucity of data describing the -molecular architecture of the human HYP, especially in the context of -sex-differentiated cell types that drive evolutionarily essential, -hypothalamus-mediated behaviors in males and females.

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This study, led by Bernard (Bernie) Mulvey, Kristen Maynard, and -Kasper Hansen, profiled the adult human mediobasal hypothalamus -(ventromedial nucleus, VMH, and arcuate nucleus, ARC) using Visium and -Xenium spatial transcriptomic platforms (10x Genomics). Atlasing and -sex-differential expression efforts using Visium data from 8 donors (4 -per sex) were used to guide gene selection for subsequent Xenium assays -on adjacent tissue sections from these same 8 donors.

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-Experimental Overview -
Experimental Overview
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Examining 13 Xenium samples revealed 5 ARC and 4 VMH neuronal -populations governing known hypothalamus-specific functions and defined -their spatial distributions. Examinining the full dataset of 23 samples, -human VMH and ARC demonstrated increases in retinoid pathway gene -expression relative to mouse. Sex-DE analyses of VMH and ARC revealed -correlated autosomal expression differences, which were localized to -ESR1- and TAC3-expressing neurons in the ARC, and -CRHR2-expressing neurons in the VMH. VMH- and ARC-residing cell -types have a striking number of sex-DE genes linked to sex-biased -disorders, including autism, depression, and schizophrenia. By mapping -disease associations to hypothalamic regions containing cell types with -established roles in mediating sex-divergent physiology and behavior, -these data provide insights into mechanistic bases of sex bias in -neurodevelopmental and neuropsychiatric disorders.

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Sex DE Analysis with Xenium Sex-DE analysis was performed -at the level of Xenium clusters by first subsetting to all cells within -the boundaries of the VMH or ARC. Then, cells of each type are tested -separately for sex-DE within that domain. Thus, broadly distributed cell -clusters/types (e.g., glia) are tested for sex-DE in each domain. -Meanwhile, sex-DE testing of domain-specific neuronal clusters -(e.g., TAC3-ESR1 in ARC) is filtered to the cells -given that label and found in their domain (i.e. in the expected -anatomic space). This simplified schematic only shows one -domain-specific cluster each for ARC and VMH.

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Overview

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Welcome to the spatial_HPC project! In this study, we +generated spatially-resolved transcriptomics (SRT) and single-nucleus +RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the +anterior human hippocampus across ten adult neurotypical donors. SRT +data was generated using 10x +Genomics Visium (n=36 capture areas) and 10x +Genomics Visium Spatial Proteogenomics (SPG) (n=8 +capture areas). snRNA-seq data was generated using 10x +Genomics Chromium (n=26 total snRNA-seq +libraries).

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If you tweet about this website, the data or the R package please use +the #spatial_HPC hashtag. You can find previous tweets that +way as shown +here.

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Thank you for your interest in our work!

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Data resources

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Analysis and plotting code
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Code for analyses is contained within subdirectories of this -repository: - Visium: spatial_HYP -- Xenium: xenium_HYP -- For manuscript plots: manuscript_plot_code -- For KISS1-ESR1-TAC3 smFISH analysis: here

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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) 10ξm 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) 10ξm 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 +100ξm 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). (This figure was created with Biorender)

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Data visualization
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Interactive web portals (one for Visium, one for Xenium) have been -made available using Samui to -allow visualization of gene expression and cluster assignments, as well -as creation of custom spatial annotations. Documentation is built into -these respective visualization tools, which can be found at:

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Interactive Websites

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All of these interactive websites are powered by open source +software, namely:

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We provide the following interactive websites, organized by dataset +with software labeled by emojis:

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Supplemental Data S1-S6 and smFISH microscopy
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Supplemental data mentioned in the manuscript, along with smFISH -images on Visium/Xenium-adjacent tissue for LAMP5 and KISS1, are -available through are available through http://research.libd.org/globus/ -via the Globus endpoint jhpce#HYP_suppdata. Readme files for these data -are also available through the endpoint.

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Further data availability
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FASTQ files from Visium and unfiltered sample-level xeniumranger 1.7 -outputs (transcript-level data) compatible with Xenium Explorer software -are respectively available through GEO accessions GSE280316 -and GSE280460. -Addditional processed data may be added to the Globus endpoint in the -process of review and publication.

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Data Access

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All data, including raw FASTQ files and +SpaceRanger/CellRanger processed data outputs, +can be accessed via Gene Expression Omnibus (GEO) under accessions GSE264692 +(SRT) and GSE264624 +(snRNA-seq).

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The spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data can also be accessed through the bioconductor +package at humanHippocampus2024

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Contact

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We value public questions, as they allow other users to learn from +the answers. If you have any questions, please ask them at LieberInstitute/spatial_hpc/issues +and refrain from emailing us. Thank you again for your interest in our +work!

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How to Cite

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PENDING

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Internal

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  • JHPCE location: +/dcs04/lieber/lcolladotor/spatialHPC_LIBD4035/spatial_hpc
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Files:

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  • code: Scripts for running all analyses.
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  • plots: plots generated by analysis scripts.
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  • processed-data +
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    • Images: images used for running +SpaceRanger and VistoSeg.
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    • spaceranger: SpaceRanger output +files.
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  • raw-data +
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    • sample_info: metadata about samples.
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  • snRNAseq_HPC: code, plots, and data for snRNA-seq +analyses.
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  • Code for running GraphST +clustering pipeline can be found here: https://github.com/JianingYao/SpatialHPC_graphST_multipleSample
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This GitHub repository is organized along the R/Bioconductor-powered +Team Data Science group guidelines. It follows the LieberInstitute/template_project +structure.

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How to Cite

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