Dec 04, 2024

Public workspaceATAC-seq protocol

DOI
dx.doi.org/10.17504/protocols.io.14egn924ml5d/v1
  • 1Sloan Kettering Institute;
  • 2Johns Hopkins University
  • IGVF
Michael Beer
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DOI: dx.doi.org/10.17504/protocols.io.14egn924ml5d/v1
Protocol Citation: Renhe Luo, Michael Beer, Danwei Huangfu 2024. ATAC-seq protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.14egn924ml5d/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: December 04, 2024
Last Modified: December 04, 2024
Protocol Integer ID: 113699
Funders Acknowledgements:
NHGRI
Grant ID: U01HG012051
Abstract
ATAC-seq protocol for ESC-DE differentiation
ATAC-seq protocol
ATAC-seq protocol
50K cryopreserved cells were washed in cold PBS and lysed.
The transposition reaction containing TDE1 Tagment DNA Enzyme (Illumina; 20034198) was incubated at 37°C for 30 minutes.
The DNA was purified with the MinElute PCR Purification Kit (QIAGEN; 28004) and amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs; M0541L).
After evaluation by real-time PCR, 3-14 additional PCR cycles were done.
The final product was cleaned by AMPure XP beads (Beckman Coulter; A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio.
Libraries were sequenced on a HiSeq 4000 or NovaSeq 6000 platform in a PE50 run, using the HiSeq 3000/4000 SBS Kit or NovaSeq 6000 S1 Reagent Kit (100 Cycles) (Illumina).