Neural Organoid Hormonal Atlas (NOHA)

Exploration of gene expression in Cheroni et al. 2022 bulk RNA-Seq dataset.

Exploration of gene expression patterns in the BrainSpan dataset.

Castaldi et al. 2025 scRNA-seq dataset - force directed graph.

Initial exploration of the Castaldi et al. 2025 scRNA-Seq dataset.

SEACells for metacell generation from the Castaldi et al. 2025 scRNA-Seq dataset.

Exploration of gene expression in metacells from the Castaldi et al. 2025 scRNA-Seq dataset.

SEACells-based analysis of day 50 samples in Castaldi et al. 2025 dataset.

Subsetting and preprocessing of HNOCA dataset from He et al. 2024.

Exploration in HNOCA dataset after subset by age <= 50 DIV.

Data preparation for SEACells analysis on HNOCA dataset.

Generation of metacells using SEACells for HNOCA dataset and gene expression exploration in metacells.

Exploratory analysis of Wang et al. 2025 scRNA-seq dataset.

SEACells analysis of first trimester samples in Wang et al. dataset.

SEACells analysis of second trimester samples in Wang et al. dataset.

SEACells analysis of third trimester samples in Wang et al. dataset.

Gene expression exploration in metacells for first trimester samples.

Gene expression exploration in metacells for second trimester samples.

Gene expression exploration in metacells for third trimester samples.

Exploratory quality control of bulk RNA-Seq data for CTL04.

Sample correlation heatmap for CTL04 bulk RNA-seq dataset.

Exploratory quality control of bulk RNA-Seq data for CTL08.

Sample correlation and PCA analysis including batch effects for CTL08 dataset.

Main gene signatures for CTL04 bulk RNA-Seq dataset.

Metabolism gene signatures for CTL04.

Receptor gene signatures for CTL04.

Target gene signatures for CTL04.

Main gene signatures for CTL08 bulk RNA-Seq dataset.

Metabolism gene signatures for CTL08.

Receptor gene signatures for CTL08.

Target gene signatures for CTL08.

DESeq2 differential expression analysis of CTL04 bulk RNA-Seq dataset.

DESeq2 differential expression analysis of CTL08 bulk RNA-Seq dataset.

topGO GO enrichment for AHR pathway - agonist vs DMSO (CTL04).

topGO GO enrichment for AHR pathway - agonist vs inhibitor vs DMSO (CTL04).

topGO GO enrichment for AHR pathway - inhibitor vs DMSO (CTL04).

topGO GO enrichment for Androgen pathway - agonist vs DMSO (CTL04).

topGO GO enrichment for Androgen pathway - agonist vs inhibitor vs DMSO (CTL04).

topGO GO enrichment for Estrogen pathway - agonist vs inhibitor vs DMSO (CTL04).

topGO GO enrichment for Estrogen pathway - inhibitor vs DMSO (CTL04).

topGO GO enrichment for Glucocorticoid pathway - agonist vs inhibitor vs DMSO (CTL04).

topGO GO enrichment for Glucocorticoid pathway - inhibitor vs DMSO (CTL04).

topGO GO enrichment for Liver X receptor pathway - agonist vs inhibitor vs DMSO (CTL04).

topGO GO enrichment for Liver X receptor pathway - inhibitor vs DMSO (CTL04).

topGO GO enrichment for Retinoid pathway - agonist vs DMSO (CTL04).

topGO GO enrichment for Retinoid pathway - agonist vs inhibitor vs DMSO (CTL04).

topGO GO enrichment for Retinoid pathway - inhibitor vs DMSO (CTL04).

topGO GO enrichment for Thyroid pathway - agonist vs DMSO (CTL04).

topGO GO enrichment for Thyroid pathway - agonist vs inhibitor vs DMSO (CTL04).

topGO GO enrichment for Thyroid pathway - inhibitor vs DMSO (CTL04).

topGO GO enrichment for AHR pathway - agonist vs inhibitor vs DMSO (CTL08).

topGO GO enrichment for Estrogen pathway - agonist vs DMSO (CTL08).

topGO GO enrichment for Glucocorticoid pathway - agonist vs inhibitor vs DMSO (CTL08).

topGO GO enrichment for Glucocorticoid pathway - inhibitor vs DMSO (CTL08).

topGO GO enrichment for Liver X receptor pathway - agonist vs DMSO (CTL08).

topGO GO enrichment for Liver X receptor pathway - agonist vs inhibitor vs DMSO (CTL08).

topGO GO enrichment for Retinoid pathway - agonist vs DMSO (CTL08).

topGO GO enrichment for Retinoid pathway - agonist vs inhibitor vs DMSO (CTL08).

topGO GO enrichment for Thyroid pathway - agonist vs DMSO (CTL08).

topGO GO enrichment for Thyroid pathway - agonist vs inhibitor vs DMSO (CTL08).

topGO GO enrichment for Thyroid pathway - inhibitor vs DMSO (CTL08).

Scatterplots comparing DEGs between CTL04 and CTL08.

Overlap of differentially expressed genes for CTL04.

Heatmaps of overlapping DEGs for CTL04.

Overlap of differentially expressed genes for CTL08.

WGCNA network construction for bulk RNA-Seq.

Characterization of WGCNA modules for bulk RNA-Seq.

Functional analysis of WGCNA modules for bulk RNA-Seq.

Load Cell Ranger outputs into the scRNA-Seq workflow.

Integrate scRNA-Seq datasets.

Stress signature analysis.

Stress signature analysis - androgen.

Quality control and filtering of scRNA-Seq data.

Exploratory analysis - control samples.

Exploratory analysis - hormones samples.

Exploratory analysis - androgen samples.

Highly variable genes.

Highly variable genes - androgens.

Exploration of gene signatures, including hormone- and metabolism-related genes, in scRNA-seq data.

Androgen substudy - differential abundance.

Hormones substudy - differential expression analysis for neurons.

Hormones substudy - differential expression analysis for progenitors.

Hormones substudy - differential abundance analysis and WGCNA for progenitors.

Hormones substudy - differential abundance analysis and WGCNA for neurons.

Functional characterization of WGCNA modules from scRNAseq dataset.

PCA of morphological features of nuclei.

Comparison of proliferation and neuronal markers across exposures in IF.

Representative images of antibodies MIX1 exposed organoids.

Representative images of antibodies MIX2 exposed organoids.

Visualization of steroidomics data.

Comparison of steroidomics data with weighted gene co-expression analysis modules from bulkRNA-seq.