The University of Auckland
Farrow_etal_supplementarytables_010224.xlsx (3.5 MB)

Farrow et al Supplementary tables 1 - 13

Download (3.5 MB)
Version 2 2024-02-01, 00:24
Version 1 2023-12-21, 00:11
posted on 2024-02-01, 00:24 authored by Sophie FarrowSophie Farrow

Farrow et al Supplementary tables:

  1. All oligonucleotides included in the synthesied library (Agilent), see phenotype abbreviation descriptors above table
  2. 78 PD GWAS loci identified by Nalls et al 2019, and the number of elements tested per locus. Rows 82-95 show GWAS loci identified by Nalls et al that did not pass final QC, but were included in the library
  3. 21 PARK genes and summary data on the number of eQTLS identified in the brain, associated with the expression of these PARK genes
  4. CoDeS3D output data highlighting all putative regulatory eQTLs associated with the expression of one or more of the PARK genes in brain cell-types and tissues
  5. Summary data from Booms et al. highlighting putative regulatory SNPs in microglia
  6. MPRA identified general enhancers, based on Z-score calculations (+/- 3SD)
  7. Allele specific enhancers (<0.05, MPRAlm tool) identified in HEK293 cells. LD tag SNP listed where the SNP was a PDGWAS_LD SNP.
  8. Elements excluded from allele-specific mpralm analysis due to insufficient barcode numbers for either the ref or alt allele
  9. Mean depletion rank score for each element (SNP) included in the MPRA oligonucleotide library
  10. FABIAN prediction analysis to identify which allele-specific regulatory elements may disrupt a transcription factor binding site
  11. Epigenomic and regulatory annotations of the allele-specific and general enhancer sites, data obtained from Haploreg
  12. CoDeS3D output data highlighting significant eQTLS for each of the allele-specific and general enhancer SNPs. Analysis was run across all tissues within the GTEx database and all Hi-C cell-types available (see doi: 10.1093/brain/awac022 for more details)
  13. Differentially expressed genes in the KOLF.21J iPSC line for three of the MPRA identified allele-specific enhancers (rs11646653, rs78222414, rs3815082). Gene expression is compared between 3 replicates of the edited clones vs. 9 replicates of the WT cell line.



University of Auckland