Study design.
Number of samples from each pair of sample-level variables. See Table S18 for sample variable description.
Samples used for downstream analyses.
Number of samples from each pair of sample-level variables after sample filtering based on QC metrics and PCA plots. See Table S18 for sample variable description.
DEGs in the nicotine-exposed pup brain.
Metadata of DEGs in the nicotine pup brain and their logFC, moderated t-stats, p-value, and adjusted p-value for DE. The statistics were computed with topTable() from limma; see its documentation for the definition of the variable names. Data from this table were used to create the volcano plot in Figure 2A.
Created here.
DEGs in the smoking-exposed pup brain.
Same as in Table S3 but for DEGs in the smoking pup brain. Data from this table were used to create the volcano plot in Figure 2B.
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Differential gene expression results for the complete gene dataset.
Gene-level metadata and the logFC, moderated t-stats, p-value, and adjusted p-value for DE of each gene in the 5 experimental groups: nicotine vs vehicle exposure in pup brain, smoking exposure vs control in pup brain, nicotine vs vehicle administration in adult brain, smoking exposure vs control in adult brain, and smoking exposure vs control in adult blood. Also included are the replication results of the genes in mouse blood. The statistics were computed with topTable() from limma; see its documentation for the definition of the variable names. Scatter plots of t-stats in Figure 2C, Figure 4 and Figure 21A-B can be reproduced with the data provided in this table.
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Differentially expressed transcripts in the nicotine-exposed pup brain.
Metadata of DE transcripts in the nicotine pup brain and their logFC, moderated t-stats, p-value, and adjusted p-value. The statistics were computed with topTable() from limma; see its documentation for the definition of the variable names.
Created here.
Differentially expressed transcripts in the smoking-exposed pup brain.
Same as in Table S6 but for DE transcripts in the smoking pup brain.
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Differential expression of transcripts vs genes for the nicotine experiment in pup brain.
DE statistics (logFC, moderated t-stats, p-value, and adjusted p-value) for transcripts and their respective genes for nicotine exposure in pup brain, and if transcripts and genes were both or solely DE. Only transcripts of genes present in the gene dataset are shown. The statistics were computed with topTable() from limma; see its documentation for the definition of the variable names. Scatter plot of nicotine t-stats in Figure 3A can be reproduced with the data contained in this table.
Created here.
Differential expression of transcripts vs genes for the smoking experiment in pup brain.
Same as in TableS8 but for the smoking experiment. Scatter plot of smoking t-stats in Figure 3A can be reproduced with the data contained in this table.
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Differentially expressed exons in the nicotine-exposed pup brain.
Metadata of DE exons in the nicotine pup brain and their logFC, moderated t-stats, p-value, and adjusted p-value. The statistics were computed with topTable() from limma; see its documentation for the definition of the variable names.
Created here.
Differentially expressed exons in the smoking-exposed pup brain.
Same as in Table S10 but for DE exons in the smoking pup brain.
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Differential expression of exons vs genes for the nicotine experiment in pup brain.
DE statistics (logFC, moderated t-stats, p-value, and adjusted p-value) for exons and their respective genes for nicotine exposure in pup brain, as well as if exons and genes were both DE or not. Only exons of genes present in the gene dataset are shown. The statistics were computed with topTable() from limma; see its documentation for the definition of the variable names. Scatter plot of nicotine t-stats in Figure 3B can be reproduced with the data contained in this table.
Created here.
Differential expression of exons vs genes for the smoking experiment in pup brain.
Same as in Table S12 but for the smoking experiment. Scatter plot of smoking t-stats in Figure 3B can be reproduced with the data contained in this table.
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Differentially expressed exon-exon junctions in the nicotine-exposed pup brain.
Metadata of DE exon-exon junctions in the nicotine pup brain, including for each:
- if both the donor and acceptor sites together are known and annotated in GENCODE M25 (
inGencodevariable); - if the donor and acceptor sites are individually annotated in GENCODE M25 (
inGencodeStartandinGencodeEndvariables, respectively); - the junction
Class: Novel (if both start and end sites are unknown, also known as fully novel junctions), InGen (already annotated in GENCODE M25), AltStartEnd (if it has only one known site), or ExonSkip (with sites from non-successive exons, both known individually but not together), and - if they are fusion junctions, meaning that they connect exons from different genes (
isFusionvariable).
Their logFC, moderated t-stats, p-value, and adjusted p-value are provided. These statistics were computed with topTable() from limma; see its documentation for the definition of the variable names.
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Differentially expressed exon-exon junctions in the smoking-exposed pup brain.
Same as in Table S14 but for DE exon-exon junctions in the smoking pup brain.
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Differential gene expression results for gene pairs of mouse-human orthologs.
The logFC, moderated t-stats, p-value, and adjusted p-value of the human gene for smoking exposure in the prenatal and adult human brain, and for the corresponding mouse orthologous gene for the 5 experimental mice groups (as in Table S5), are presented. Only mouse genes with human ortholog(s) present in the human dataset from Semick et al., 2020 are considered. The DE statistics were computed with topTable() from limma; see its documentation for the definition of the variable names. Figure 5 and Figure 21C were created with the data this table provides.
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Mouse DEGs in pup brain with human orthologs TUD-associated.
Pup brain DEGs for the nicotine and smoking exposure with human orthologs that were the nearest genes of genome-wide significant (GWS) lead SNPs in loci associated with Tobacco Use Disorder (TUD), obtained from a multi-ancestral GWAS meta-analysis of TUD cases and controls in individuals from 8 cohorts (including UKBB), with European (EUR), African American (AA), and Latin American (LA) ancestry (TUD-multi+UKBB dataset), and from a within-ancestry GWAS meta-analysis in EUR individuals from 5 cohorts, including UKBB data (TUD-EUR+UKBB dataset). As well as human genes significantly associated with TUD in EUR individuals (TUD-EUR-MAGMA dataset); neurobiologically relevant target human genes associated with TUD (TUD-EUR-H-MAGMA dataset), especially expressed in prenatal (TUD-EUR-H-MAGMA-prenatal dataset) and adult brain (TUD-EUR-H-MAGMA-adult dataset); TUD-associated human genes whose expression is predicted to be affected by EUR-SNPs across multiple brain regions (TUD-EUR-S-MultiXcan dataset) and in specific brain regions (TUD-EUR-S-PrediXcan dataset), including the frontal cortex (TUD-EUR-S-PrediXcan-FC dataset). See more details of these TUD-associated human genes in the original publication (Toikumo et al., 2023).
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Dictionary of sample variables.
Description of the sample variables used throughout this project.
Associated genes of fully novel DE exon-exon junctions in pup brain.
Nearest, following, and preceding genes of the fully novel DE exon-exon junctions without assigned gene for the nicotine and smoking exposure in pup brain.
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