MyND RNAseq and eQTL results

This dataset is part of the manuscript: "Dysregulation of mitochondrial and proteo-lysosomal genes in Parkinson's disease myeloid cells", by Navarro E, Udine E, et al.

Description of files:

• MyND_monocyte.cis_eqtl_nominal.txt.gz - Full nominal eQTL summary statistics (gzip-compressed)
• MyND_monocyte.cis_eqtl_permuted.txt.gz - Full permuted eQTL summary statistics (gzip-compressed)
• MyND_monocyte.cis_sqtl_nominal.txt.gz - Full nominal sQTL summary statistics (gzip-compressed)
• MyND_monocyte.cis_sqtl_permuted.txt.gz - Full permuted sQTL summary statistics (gzip-compressed)
• gencode.v30.primary_assembly.annotation.txt.gz - Gencode (v30) gene annotations used in the analysis (gzip-compressed)
• monocyte_counts_matrix.txt.gz - RSEM counts from monocytes samples (230 samples) (gzip-compressed)
• monocyte_tpms_matrix.txt.gz -RSEM TPMs  from monocytes samples (230 samples) (gzip-compressed)
• microglia_counts_matrix.txt.gz - RSEM counts from microglia samples (128 samples - 55 donors) (gzip-compressed)
• microglia_tpms_matrix.txt.gz - RSEM TPMs from microglia samples (128 samples - 55 donors) (gzip-compressed)
• processed_seurat_obj.RDS - Seurat R data object file containing single-cell RNA-seq results (14,827 features, 19,144 cells, 10 donors)

Table columns are formatted as follows:

Nominal eQTL results include all SNP-gene pairs tested (using a 1Mb window from each side of the transcription start site (TSS) of a gene). Table columns are formatted as follows:

1. "pheno_id" - The phenotype ID
2. "pheno_chr" - The chromosome ID of the phenotype
3. "pheno_start" - The start position of the phenotype
4. "pheno_end" - The end position of the phenotype
5. "pheno_strand" - The strand orientation of the phenotype
6. "num_var" - The total number of variants tested in cis
7. "distance" - The distance between the phenotype and the tested variant (accounting for strand orientation)
8. "snp_id" - The ID of the tested variant
9. "snp_chr" - The chromosome ID of the variant
10. "snp_start" - The start position of the variant
11. "snp_end" - The end position of the variant
12. "nominal_pval" - The nominal P-value of association between the variant and the phenotype
13. "slope" - The corresponding regression slope
14. "lead_snp" - A binary flag equal to 1 is the variant is the top variant in cis

Permuted eQTL results include only the top SNP-gene association for each gene (1000 permutations). Table columns are formatted as follows:

1. "gene_id" - The phenotype ID
2. "gene_chr" - The chromosome ID of the phenotype
3. "gene_start" - The start position of the phenotype
4. "gene_end" - The end position of the phenotype
5. "gene_strand" - The strand orientation of the phenotype
6. "num_var" - The total number of variants tested in cis
7. "distance" - The distance between the phenotype and the tested variant (accounting for strand orientation)
8. "snp_id" - The ID of the top variant
9. "snp_chr" - The chromosome ID of the top variant
10. "snp_start" - The start position of the top variant
11. "snp_end" - The end position of the top variant
12. "degree_of_freedom" - The number of degrees of freedom used to compute the P-values
13. "dummy" - Dummy
14. "bval1" - The first parameter value of the fitted beta distribution
15. "bval2" - The second parameter value of the fitted beta distribution (it also gives the effective number of independent tests in the region)
16. "nominal_pval" - The nominal P-value of association between the phenotype and the top variant in cis
17. "slope" - The corresponding regression slope
18. "empirical_pval" - The P-value of association adjusted for the number of variants tested in cis given by the direct method (i.e. empirircal P-value)
19. "beta_dist_pval" - The P-value of association adjusted for the number of variants tested in cis given by the fitted beta distribution. We strongly recommend to use this adjusted P-value in any downstream analysis

Nominal sQTL results include all SNP-junction pairs tested (using a 100kb window from the center of each intron cluster). Table columns are formatted as follows:

1. "pheno_id" - The phenotype ID
2. "pheno_chr" - The chromosome ID of the phenotype
3. "pheno_start" - The start position of the phenotype
4. "pheno_end" - The end position of the phenotype
5. "pheno_strand" - The strand orientation of the phenotype
6. "num_var" - The total number of variants tested in cis
7. "distance" - The distance between the phenotype and the tested variant (accounting for strand orientation)
8. "snp_id" - The ID of the tested variant
9. "snp_chr" - The chromosome ID of the variant
10. "snp_start" - The start position of the variant
11. "snp_end" - The end position of the variant
12. "nominal_pval" - The nominal P-value of association between the variant and the phenotype
13. "slope" - The corresponding regression slope
14. "lead_snp" - A binary flag equal to 1 is the variant is the top variant in cis

Permuted sQTL results include only the top SNP-junction association by gene (1000 permutations). Table columns are formatted as follows:

1. "pheno_id" - The phenotype group ID (here a gene ID)
2. "pheno_chr" - The chromosome ID of the phenotype group
3. "pheno_start" - The start position of the phenotype group
4. "pheno_end" - The end position of the phenotype group
5. "pheno_strand" - The strand orientation of the phenotype group
6. "pheno_id" - The top phenotype in the group (here an exon ID)
7. "num_pheno" - The total number of phenotypes in the group (i.e. #exons)
8. "num_var" - The total number of variants tested in cis
9. "distance" - The distance between the phenotype group and the tested variant (accounting for strand orientation)
10. "snp_id" - The ID of the top variant
11. "snp_chr" - The chromosome ID of the top variant
12. "snp_start" - The start position of the top variant
13. "snp_end" - The end position of the top variant
14. "degree_of_freedom” - The number of degrees of freedom used to compute the P-valuesm"
15. "dummy" - Dummy
16. "bval1" - The first parameter value of the fitted beta distribution
17. "bval2" - The second parameter value of the fitted beta distribution (it also gives the effective number of independent tests in the region)
18. "nominal_pval" - The nominal P-value of association between the top phenotype and the top variant in cis
19. "slope" - The corresponding regression slope
20. "empirical_pval" - The P-value of association adjusted for the number of variants and phenotypes tested in cis given by the direct method (i.e. empirircal P-value)
21. "beta_dist_pval" - The P-value of association adjusted for the number of variants and phenotypes tested in cis given by the fitted beta distribution. We strongly recommend to use this adjusted P-value in any downstream analysis

NOTE: The effect sizes of eQTLs and sQTL are defined as the effect of the alternative allele (ALT) relative to the reference (REF) allele in the human genome reference (GRCh38).