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madhavitippani authored Dec 9, 2024
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Expand Up @@ -394,18 +394,27 @@ <h2>Study design</h2>
(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&amp;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&amp;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). (This figure was created with <a href="https://biorender.com">Biorender</a>)</p>
(B) Tissue blocks were scored and cryosectioned for snRNA-seq assays (gold),
and placement on Visium slides (Visium H&amp;E, blue). (C) Top: Tissue sections
(2-4 100μm cryosections per donor) from all ten donors were collected from the
same tissue blocks for measurement with the 10x Genomics Chromium 3’ gene
expression platform. For each donor, two samples were generated, one sorted
based on propidium iodide (PI, purple) and the second sorted based on PI+ and
NeuN+ (green). Replicate samples were collected from three donors for a total
of n=26 total snRNA-seq libraries. Bottom: 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. Orientation was verified based on expression of known marker genes.
(D) Canonical marker genes were identified as spatially variable genes using nnSVG.
(E) SRT data was clustered using PRECAST (30) with k=18 and clusters were annotated
(columns) based on expression of known marker genes (rows). Cluster groupings
indicated at the top of the heatmap define which clusters contributed to the
broad domains of Neuron, Neuropil, white matter (WM), and vascular/ cerebrospinal
fluid cell-enriched (Vasc/CSF). RHP: retrohippocampus, SUB: subiculum, CA2.4:
cornu ammonis (CA) regions 2 through 4 (CA2, CA3, CA4), GCL: dentate gyrus
granule cell layer, ML: dentate gyrus molecular layer, SL: stratum lucidum,
SR: stratum radiatum, SLM: stratum lacunosum-moleculare, SGZ: dentate gyrus
subgranular zone.</p>
</div>
<div id="interactive-websites" class="section level2">
<h2>Interactive Websites</h2>
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