ATAC-seq Protocol for Chromatin Profiling

ATAC-seq was performed as previously described^{30 (link)}. 20,000 unfixed nuclei were tagged using Tn5 transposase (Nextera DNA sample prep kit; Illumina) for 30 min at 37°C, and the resulting library fragments were purified using a Qiagen MinElute kit. Libraries were amplified by 10–12 PCR cycles, purified using a Qiagen PCR cleanup kit, and finally sequenced on an Illumina HiSeq 2500 with 75 bp paired-end reads to a minimum depth of 30 million reads per sample. At least two technical replicates were processed per biological sample.

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Caielli S., Troggian Veiga D., Balasubramanian P., Athale S., Domic B., Murat E., Banchereau R., Xu Z., Chandra M., Chung C.H., Walters L., Baisch J., Wright T., Punaro M., Nassi L., Stewart K., Fuller J., Ucar D., Ueno H., Zhou J., Banchereau J, & Pascual V. (2018). A CD4+ T cell population expanded in Lupus blood provides B cell help through IL10 and succinate. Nature medicine, 25(1), 75-81.

Publication 2018

Nextera DNA sample prep kit MinElute kit PCR cleanup kit HiSeq 2500

Atac seq Library Nuclei Tn5 transposase

Corresponding Organization :

Other organizations : Baylor University, Jackson Laboratory, Cornell University, Texas Scottish Rite Hospital for Children

Top 5 similar protocols

Variable analysis

independent variables

Tn5 transposase (Nextera DNA sample prep kit; Illumina)

dependent variables

Library fragments
Sequencing depth (minimum of 30 million reads per sample)

control variables

Number of nuclei (20,000 unfixed nuclei)
Tagmentation time (30 min at 37°C)
Number of PCR cycles (10–12)
Technical replicates (at least two per biological sample)

controls

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

Annotations

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