ATAC-seq from Low-Input Nuclei

ATAC-seq60 (link) was performed in two biological replicates per condition from 5 × 10⁴ nuclei per replicate using Nextera Tn5 Transposase (Illumina FC-121-1030, 30 min, 37º). DNA was purified by Qiagen MinElute Kit. Transposed fragments were amplified with NEBNext High-Fidelity PCR Master Mix (NEB M0541). Libraries were cleaned and size-selected using AMPure beads (Agilent) and assessed by Bioanalyzer and Qubit.

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Cuartero S., Weiss F.D., Dharmalingam G., Guo Y., Ing-Simmons E., Masella S., Robles-Rebollo I., Xiao X., Wang Y.F., Barozzi I., Djeghloul D., Amano M.T., Niskanen H., Petretto E., Dowell R.D., Tachibana K., Kaikkonen M.U., Nasmyth K.A., Lenhard B., Natoli G., Fisher A.G, & Merkenschlager M. (2018). Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nature immunology, 19(9), 932-941.

Publication 2018

MinElute Kit NEBNext High-Fidelity PCR Master Mix AMPure beads

Atac Biological Nuclei Replicate Tn5 transposase

Corresponding Organization :

Other organizations : MRC London Institute of Medical Sciences, Imperial College London, European Institute of Oncology, University of Eastern Finland, University of Colorado Boulder, University of Oxford, Humanitas University

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Variable analysis

independent variables

Biological condition (unknown)

dependent variables

ATAC-seq signals (chromatin accessibility)

control variables

Number of nuclei per replicate (5 × 10^4)
Nextera Tn5 Transposase (Illumina FC-121-1030, 30 min, 37°C)
DNA purification method (Qiagen MinElute Kit)
Library amplification method (NEBNext High-Fidelity PCR Master Mix, NEB M0541)
Library cleaning and size-selection method (AMPure beads, Agilent)
Library quality assessment (Bioanalyzer and Qubit)

controls

No positive controls mentioned
No negative controls mentioned

Annotations

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