Online Tables for the thesis "Deconvoluting Bulk RNA-seq Data to Uncover Cell-Type Specific Signatures in Depression" by Roie Dvir

This repository contains the online tables that accompany my thesis, "Deconvoluting Bulk RNA-seq Datato Uncover Cell-Type Specific Signatures in Depression." In the following, I list the description of all tables: The data is divided into seven files. The first file (sig genes DEA thesis Roie Dvir) includes all the tables of significant genes (FDR < 0.1) of the DE analyses conducted by DESeq2. 1. Significant genes for status (228 individuals with depression vs. 33 controls) of the bulk RNA-seq data. 2. Significant genes for age as the main variable of the bulk RNA-seq data. 3. Significant genes for CRP level as the main variable of the bulk RNA-seq data 4. Significant genes for status (individuals with depression vs. controls) of the downsampled bulk RNA-seq data (66 total samples). 5. Significant genes for age as the main variable of the downsampled bulk RNA-seq data (66 total samples). 6. Significant genes for CRP as the main variable of the downsampled bulk RNA-seq data (66 total samples). 7. Significant genes for age as the main variable of the bulk RNA-seq data, including the first three PCs of the data's cell type estimates. 8. Significant genes for CRP as the main variable of the bulk RNA-seq data, including the first three PCs of the data's cell type estimates. 9. Significant genes for status (individuals with depression vs. controls) of the downsampled bulk RNA-seq data (66 total samples), including the first three PCs of the data's cell type estimates. 10. Significant genes for age as the main variable of the downsampled bulk RNA-seq data (66 total samples), including the first three PCs of the data's cell type estimates. 11. Significant genes for CRP as the main variable of the downsampled bulk RNA-seq data (66 total samples), including the first three PCs of the data's cell type estimates. 12. Significant transcripts for age as the main variable of the bulk transcript-level RNA-seq data. 13. Significant transcripts for CRP as the main variable of the bulk transcript level RNA-seq data. 14. Significant transcripts for status (individuals with depression vs. controls) of the downsampled bulk transcript level RNA-seq data (66 total samples). 15. Significant transcripts for age as the main variable of the downsampled bulk transcript-level RNA-seq data (66 total samples). 16. Significant transcripts for CRP as the main variable of the downsampled bulk transcript-level RNA-seq data (66 total samples). The rest of the files (6) are divided by cell types. Each file contains the tables of the significant genes identified by the cell-type-specific DE methods. For each cell type, there are the results for status, age, CRP, and BMI. If there were no significant genes identified for any of the tests, they are not included.