38 datasets found

  • Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-s...

    The University of Auckland
    In this project, we design a methods to detect novel transcripts integrating ab initio prediction on genomic sequences and filtration with various RNA-seq data. 100 splice sites were selected and RT-PCR on 48 human tissues and cell lines (including a blank negative control) were conducted. The product of the same tissue or cell line were mixed and...
    Created 1 August 2019 Updated 1 October 2022
  • IGV_views.tar.zip

    The University of Auckland
    IGV viewing files to view genomic features of the human ribosomal DNA (rDNA) such as conservation with primates, transcripts, chromatin features, and repeats. As part of a comparative genomics study to identify potential functional elements in the human rDNA IGS by phylogenetic footprinting.
    Created 1 August 2019 Updated 1 October 2022
  • Spatial eQTL data for GWAS traits

    The University of Auckland
    Spatial eQTL data for traits in "Chromatin interactions and expression quantitative trait loci reveal genetic drivers of multimorbidity"
    Created 1 August 2019 Updated 1 October 2022
  • PhD Thesis Appendix

    The University of Auckland
    Appendix files associated with the PhD thesis "Chromatin organization and gene regulation in granulocytic cells" by Elsie Carlota Jacobson Supplementary table 1. Significantly differentially expressed genes. All genes with significantly differential gene expression (false discovery rate (FDR) <0.05) between either 5µm pores compared to control, 14µm...
    Created 1 August 2019 Updated 1 October 2022
  • Supplementary_Material_Chapter_6_Transcriptomic_response_Medicago_truncatula_...

    The University of Auckland
    Supplementary material from Chapter 6 of my thesis entitled Transcriptomic response of Medicago truncatula leaf tissue to a short day to long day shift
    Created 1 August 2019 Updated 1 October 2022
  • Supplementary Tables 1-18

    The University of Auckland
    Supplementary Tables 1-18 for the paper "Decoding the multimorbidities among psychiatric disorders and cognitive functioning"
    Created 1 December 2019 Updated 1 October 2022
  • Machine learning identifies regulatory changes in the lung as key to the conv...

    The University of Auckland
    All datasets and supplementary information for this article.
    Created 1 November 2020 Updated 1 October 2022
  • S. cerevisiae 40-rDNA copy strain

    The University of Auckland
    S. cerevisiae strain with 40 rDNA copies
    Created 1 March 2021 Updated 1 October 2022
  • Supplementary data 2. Hi-C datasets used in the study

    The University of Auckland
    Details of the Hi-C datasets from 70 cell-lines/tissues used for the analysis is provided in the table. Hi-C contact data was used to find the target genes of the autoimmune disease-associated SNPs.
    Created 1 April 2021 Updated 1 October 2022
  • Supplementary data 3. Gene regulatory interactions of the SNPs associated wit...

    The University of Auckland
    We identified cis and trans regulatory interactions of the SNPs associated with 18 AiDs through chromatin-contact data and eQTL associations. The analysis was performed on each disease separately and the results are presented here. The coordinates of the SNPs and the genes are provided according to hg38 genome assembly.
    Created 1 April 2021 Updated 1 October 2022
  • Supplementary data 4. SNP functional annotation and a list of the pleiotropic...

    The University of Auckland
    We identified that the AiD associated SNPs are located in the non-coding regions of the genome. Of those, 186 are pleiotropic SNPs (i.e., same loci associated with multiple AiDs) that were associated with more than two AiDs. Majority of them (N=60) are shared between Crohn's disease (CRD) and Ulcerative colitis (ULC). We have presented a list of...
    Created 1 April 2021 Updated 1 October 2022
  • Untangling the genetic link between type 1 and type 2 diabetes using function...

    The University of Auckland
    All datasets and supplementary information for this article.
    Created 1 November 2020 Updated 1 October 2022
  • Go with the flow: Population connectivity of the NZ scampi – raw data.

    The University of Auckland
    This is the raw GBS and particle modelling data that has been used in the article "Go with the flow: Population connectivity of the New Zealand deep sea lobster, Metanephrops challengeri". 'NZ_scampi_GBS.tar.gz' are the raw sequencing files for each scampi individual used for the population genetics section of this study.'NETCDF_data.zip' are the raw...
    Created 1 February 2021 Updated 1 October 2022
  • Chapter 3 Supplementary tables

    The University of Auckland
    This repository contains the supplementary tables for Chapter 3: Network-based identification of pleiotropic genes for Parkinson's disease and Type II Diabetes Supplementary Table 1: GWAS SNP sets used for analyses - T2D and PD Supplementary Table 2: PD GWAS: Sig. eQTLS CoDeS3D output - CNS tissues only Supplementary Table 3: PD GWAS: Sig. eQTLS...
    Created 8 August 2022 Updated 1 October 2022
  • Chapter 4 (Schierding & Farrow et al 2020; Movement Disorders) Supplementary ...

    The University of Auckland
    This repository contains the supplementary tables for chapter 4: Common variants co-regulate expression of GBA and modifier genes to delay Parkinson’s disease onset. See below for supplementary table descriptions. Supplementary Table 4.1. Hi-C datasets used in this study. List of all Hi-C datasets used in this study and their reference to original...
    Created 8 August 2022 Updated 1 October 2022
  • Chapter 5 Supplementary tables

    The University of Auckland
    This repository contains the supplementary tables for chapter 5: Mapping enhancer activity for loci marked by Parkinson’s disease variants using a Massively Parallel Reporter AssaySupplementary table 5.1: MPRA variants that have already been tested in previous MPRA studiesSupplementary table 5.2: Additional GWAS SNPs included in the assay, an extension...
    Created 8 August 2022 Updated 1 October 2022
  • ID_Chrom_Loci

    The University of Auckland
    Excel spreadsheets with four sheets, each one for a vcf file (NZ-wide, Southern specific, NI specific and SI specific), containing the Chrom ID of the corresponding locus ID in vcf files.
    Created 8 August 2022 Updated 1 October 2022
  • fasta_files

    The University of Auckland
    fasta files output from Stacks, with the sequence of the short fragments in which SNPs were identified for NZ-wide, Southern specific, NI specific and SI specific datasets. Each locus name is based on the CHROM ID of the vcf file.
    Created 8 August 2022 Updated 1 October 2022
  • Vcf_files

    The University of Auckland
    All filtered vcf files used in the analyses. File names correspond to Table S2 in the supplementary material of Salloum et al. 2022.
    Created 8 August 2022 Updated 1 October 2022
  • RDA_imputed_datasets

    The University of Auckland
    Contains the datasets used for RDA, imputed using the most common genotype within a clade NZ-wide scale (NZ.gen.imp.csv), or the most common genotype among all individuals in the Southern scale (S.gen.imp.csv), North Island scale (NI.ge.imp.csv) and South Island scale (SI.gen.imp.csv)
    Created 8 August 2022 Updated 1 October 2022
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