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HyDrop-v2-ATAC

By Suresh Poovathingal, Florian De Rop, Valerie Christiaens, Koen Theunis, Stein Aerts, PhD
View Published Protocol

Output Details

Description
This protocol details the preparation of nuclei, bulk ATAC tagmentation, microfluidics setup, HyDrop run, PCR1 cleanup, library purification, and quality control.
Identifier (DOI)
10.17504/protocols.io.x54v97mmpg3e/v1
Tags
  • DNA
  • Human
  • Single-cell ATAC-seq
Discovery Team
Team Voet
Program
Collaborative Research Network
Theme
PD Functional Genomics

Meet the Authors

  • User avatar fallback logo

    Suresh Poovathingal

    External Collaborator

  • User avatar fallback logo

    Florian De Rop

    External Collaborator

  • User avatar fallback logo

    Valerie Christiaens

    External Collaborator

  • User avatar fallback logo

    Koen Theunis

    External Collaborator

  • Stein Aerts, PhD

    Co-PI (Core Leadership): Team Voet, 

    KU Leuven

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HyDrop v2: Scalable atlas construction for training sequence-to-function models

Single-cell chromatin accessibility data helps train deep learning models to decode enhancer logic. HyDrop v2 improves data generation across species, organs, and diseases, delivering results comparable to commercial platforms like 10x Genomics.

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Nuclei isolation from brain tissue for single-cell ATAC

Protocol for isolating nuclei from brain tissue for single-cell ATAC assays like 10X Genomics Chromium Next GEM Single Cell ATAC Kit, HyDrop-ATAC, etc.

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SNP Genotyping and ApoE Genotyping

Protocol outlines DNA extraction from blood, quality control, SNP, and APOE genotyping. Adapted from PRoBaND SNP Genotyping and ApoE Genotyping Protocol by Malek et al. for Parkinson's Disease study.

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Aligning Science Across Parkinson's
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