Impact of intermittent lead exposure on hominid brain evolution

This repository contains the analysis pipeline (for bulk and single-cell RNA-Seq data) used for the paper titled "Impact of intermittent lead exposure on hominid brain evolution" published by JB et al in Science Advances.
Issues

Table of Contents

1. Overview
2. Requirements
3. Repository Structure
4. Data
5. Contact
6. Authors

Overview

This repository contains the scripts and data necessary for performing a quantification, integration and differential gene expression analysis using scRNA-Seq data and bulk RNA-Seq data. The analysis was conducted using different organoids (Cortical and Thalamic) from Homo Sapiens and Other hominids in different lead exposures (10uM and 30uM).

Requirements

The pipeline was developed using the following tools and packages. Ensure that these versions are installed before running the scripts.

Language

→ Bash

→ Python3

→ R (version 4.0 or later)

Python Packages:

→ Kallisto-Bustools

R Packages:

→ DeSeq2

→ tximport

→ readr

→ icesTAF

→ Seurat (version 5.1.0)

→ tidyverse (version 2.0.0)

→ scDblFinder (version 1.16.0)

→ RColorBrewer (version 1.1.3)

→ ggplot2

→ ggtext

→ ggnewscale

→ forcats

→ patchwork

→ Cairo

→ extrafont

→ ggpubr

→ ggrepel

Repository Structure

The pipeline was developed using the following tools and packages. Ensure that these versions are installed before running the scripts.

The repository is organized as follows:

/jb_2025_SAdv
├── bulk_RNA-seq # Scripts for bulk RNA-Seq
│   ├── degs # Differential expression analysis
│   │   ├── automate_MASTER_call.sh
│   │   ├── source_step0_MASTER.sh
│   │   ├── source_step1_TXimport.sh
│   │   ├── source_step2_DESeq2.sh
│   │   ├── st1_TXimport.R
│   │   ├── st2_DESeq2.R
│   │   ├── st3_Filters.R
│   │   └── support
│   │       ├── edit_PC-Gene_MAP.R
│   │       ├── get_DEG_table.R
│   │       ├── get_Union-DEG.R
│   │       └── merge_TXimport_PC-GeneMAP.R
│   ├── metadata
│   │   ├── map_gene_IDs.PC.tsv
│   │   ├── map_gene_IDs.raw.tsv
│   │   ├── map_gene_IDs.tsv
│   │   └── mapID2GROUP.batch2.tsv
│   ├── metrics
│   │   └── MultiQC.html
│   ├── plots
│   │   ├── automate_PCA_call.sh
│   │   ├── CMDs_chatGPT.txt
│   │   ├── CMDs_cytoscape.txt
│   │   ├── CMDs_enrichment.txt
│   │   ├── make_bubblePlot.R
│   │   ├── make_PCA_COUNTS.R
│   │   └── make_VolcanoPlot.R
│   └── pre-processing
│       ├── source_step0_MASTER.sh
│       ├── st0_Metrics.sh
│       └── st1_Kallisto.sh
├── LICENSE
├── README.md
└── scRNA-seq # Scripts for scRNA-Seq
    ├── cortical_organoids # Scripts for scRNA-Seq from cortical organoids analysis
    │   ├── 5_diff_exp_mixed_1.5_2M # Scripts for differential expression analysis
    │   │   ├── source_step1.R
    │   │   ├── source_step2.R
    │   │   ├── source_step3.R
    │   │   ├── source_step4
    │   │   └── source_step5.R
    │   ├── list_dirs.txt
    │   ├── map_genes.txt
    │   ├── sample_groups.txt
    │   ├── source_step1.R
    │   ├── source_step2.R
    │   ├── source_step3.R
    │   ├── source_step4.R
    │   ├── source_step5.R
    │   ├── source_step6.R
    │   └── source_step7.R
    ├── Organoid_Markers.tsv
    ├── source_step0_MASTER.sh
    ├── st1_KB_Ref.sh # Build Index - kb
    ├── st2_KB_Count.geneNoMM.sh # Process Data - kb
    └── thalamic_organoids # Scripts for scRNA-Seq from thalamic organoids analysis
        ├── list_dirs.txt
        ├── source_step1.R
        ├── source_step2.R
        ├── source_step3.R
        ├── source_step4.R
        ├── source_step5.R
        └── source_step6.R

Data

The raw data utilized in this pipeline is available in ENA (PRJEB83863). To download the files you should use the following command:

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/EXAMPLE/EXAMPLE/EXAMPLE.fastq.gz

Contact

Filipe F. dos Santos - (fferreira@mochsl.org.br)

Gabriela D. A. Guardia - (gguardia@mochsl.org.br)

Rafael L. V. Mercuri - (rmercuri@mochsl.org.br)

Pedro A. F. Galante - (pgalante@mochsl.org.br)

Publication

Joannes-Boyau R., de Souza J.S., Austin C., Westaway K., Moffat I., Wang W., Liao W., Zhang Y., Adams J.W., Fiorenza L., Dérognat F., Moncel M., Schwartz G.T., Bailey M., Petroski L. P., Sanchez-Sanchez S. M., Oviedo J., Herai R. H., Lemos B., Tonge M., Arora M., Muotri A. R. (2025). Impact of intermittent lead exposure on hominid brain evolution. [JOURNAL], [CAP], [PAGES]. [DOI]