Neural Organoid Hormonal Atlas (NOHA)

Html versions of the most important scripts in the GitHub repository of the Neural Organoid Hormonal Atlas.

GeneExploration_Cheroni2022

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

GeneExploration_BrainSpan

Exploration of gene expression patterns in the BrainSpan dataset.

ExplorationCastaldi

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

SEACellsCastaldi-GeneExploration

SEACells-based gene exploration in the Castaldi et al. 2025 scRNA-Seq dataset.

ExplorationPolioudakis

Initial exploration of the Polioudakis et al. 2019 scRNA-Seq dataset.

SEACellsPolioudakis-GeneExploration

SEACells-based gene exploration in the Polioudakis et al. 2019 scRNA-Seq dataset.

exploratoryQC_CTL04

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

exploratoryQC_CTL08

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

SignaturesCTL04_MainGenes

Main gene signatures for CTL04 bulk RNA-Seq dataset.

SignaturesCTL04_MetabolismGenes

Metabolism gene signatures for CTL04.

SignaturesCTL04_ReceptorGenes

Receptor gene signatures for CTL04.

SignaturesCTL04_TargetGenes

Target gene signatures for CTL04.

SignaturesCTL08_MainGenes

Main gene signatures for CTL08 bulk RNA-Seq dataset.

SignaturesCTL08_MetabolismGenes

Metabolism gene signatures for CTL08.

SignaturesCTL08_ReceptorGenes

Receptor gene signatures for CTL08.

SignaturesCTL08_TargetGenes

Target gene signatures for CTL08.

DeSeq2_CTL04

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

DeSeq2_CTL08

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

TopGO_AhHyd_Agonist_CTL04

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

TopGO_AhHyd_AgvsInh_CTL04

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

TopGO_AhHyd_Inhibitor_CTL04

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

TopGO_Andr_Agonist_CTL04

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

TopGO_Andr_AgvsInh_CTL04

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

TopGO_Estr_AgvsInh_CTL04

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

TopGO_Estr_Inhibitor_CTL04

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

TopGO_GC_AgvsInh_CTL04

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

TopGO_GC_Inhibitor_CTL04

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

TopGO_LivX_AgvsInh_CTL04

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

TopGO_LivX_Inhibitor_CTL04

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

TopGO_Ret_Agonist_CTL04

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

TopGO_Ret_AgvsInh_CTL04

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

TopGO_Ret_Inhibitor_CTL04

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

TopGO_Thyr_Agonist_CTL04

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

TopGO_Thyr_AgvsInh_CTL04

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

TopGO_Thyr_Inhibitor_CTL04

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

TopGO_AhHyd_AgvsInh_CTL08

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

TopGO_Estr_Agonist_CTL08

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

TopGO_GC_AgvsInh_CTL08

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

TopGO_GC_Inhibitor_CTL08

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

TopGO_LivX_Agonist_CTL08

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

TopGO_LivX_AgvsInh_CTL08

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

TopGO_Ret_Agonist_CTL08

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

TopGO_Ret_AgvsInh_CTL08

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

TopGO_Thyr_Agonist_CTL08

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

TopGO_Thyr_AgvsInh_CTL08

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

TopGO_Thyr_Inhibitor_CTL08

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

CTL04vsCTL08_Scatterplots

Scatterplots comparing DEGs between CTL04 and CTL08.

DEGsOverlap_CTL04

Overlap of differentially expressed genes for CTL04.

HeatmapsOverlappingDEGs_CTL04

Heatmaps of overlapping DEGs for CTL04.

DEGsOverlap_CTL08

Overlap of differentially expressed genes for CTL08.

1_NetworkGeneration

WGCNA network construction for bulk RNA-Seq.

2_ModuleCharacterization

Characterization of WGCNA modules for bulk RNA-Seq.

3_ModuleFunctional

Functional analysis of WGCNA modules for bulk RNA-Seq.

1_load_cellranger_data

Load Cell Ranger outputs into the scRNA-Seq workflow.

2_Integrate_data

Integrate scRNA-Seq datasets.

3.2_StressSignatures_filt_hormones

Stress signature analysis.

3.3_StressSignatures_filt_androgens

Stress signature analysis - androgen.

3_QC_filt

Quality control and filtering of scRNA-Seq data.

5.0_Explo_controls

Exploratory analysis - control samples.

5.1_Explo_hormones

Exploratory analysis - hormones samples.

5.4_Explo_androgen

Exploratory analysis - androgen samples.

6.1_HVGs_hormones

Highly variable genes.

6.3_HVGs_androgens

Highly variable genes - androgens.

10.1_Androgen_substudy_DA

Androgen substudy - differential abundance.

10.2_Hormones_substudy_LineMagnification_Neurons

Hormones substudy - differential expression analysis for neurons.

10.2_Hormones_substudy_LineMagnification_Progenitors

Hormones substudy - differential expression analysis for progenitors.

11.1_Hormones_substudy_LineMagnification_Progenitors_DA_divided

Hormones substudy - differential abundance analysis and WGCNA for progenitors.

11.2_Hormones_substudy_LineMagnification_Neurons_DA_divided

Hormones substudy - differential abundance analysis and WGCNA for neurons.

WGCNAModuleFunctional

Functional characterization of WGCNA modules from scRNAseq dataset.

endpoints_PCA_analysis

PCA of morphological features of nuclei.

plots_positivity_analysis_measurements

Comparison of proliferation and neuronal markers across exposures in IF.

endpoints_plot_representative_images_MIX1

Representative images of antibodies MIX1 exposed organoids.

endpoints_plot_representative_images_MIX2

Representative images of antibodies MIX2 exposed organoids.

SteroidomicsVis

Visualization of steroidomics data.

Steroidomics_WGCNA

Comparison of steroidomics data with weighted gene co-expression analysis modules form bulkRNAseq.