ATAC-seq Workflow for K562 Cells

ATAC-seq was performed essentially with 3 biological replicates as previously described [37 (link)]. Briefly, 50,000 K562 cells were collected and incubated with transposase Tn5 at 37 °C. After 1-h incubation, tagmented DNA samples were amplified using the Nextera Index kit (Illumina, FC-121-1030). DNA fractions were size selected and purified using AMPure XP beads (Beckman Coulter, A63880) according to the manufacturer’s instruction. Libraries were sequenced in paired-end with 75-nt read length using the Illumina NextSeq instrument.

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Shen J., Varshney D., Simeone A., Zhang X., Adhikari S., Tannahill D, & Balasubramanian S. (2021). Promoter G-quadruplex folding precedes transcription and is controlled by chromatin. Genome Biology, 22, 143.

Publication 2021

Nextera Index kit AMPure XP beads NextSeq instrument

Atac seq Biological K562 cells Tn5 transposase

Corresponding Organization :

Other organizations : Cancer Research UK, University of Cambridge

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Variable analysis

independent variables

Incubation of 50,000 K562 cells with transposase Tn5 at 37 °C

dependent variables

Tagmented DNA samples
DNA fractions after size selection and purification
Sequencing of libraries in paired-end with 75-nt read length using the Illumina NextSeq instrument

control variables

Incubation time (1-h)
Nextera Index kit (Illumina, FC-121-1030) for DNA amplification
AMPure XP beads (Beckman Coulter, A63880) for DNA purification

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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