Computational protocol: Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation

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Protocol publication

[…] The ATAC-seq libraries of the control and ATRA-treated cells were prepared as previously described. Briefly, the samples were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and NP-40) for 10 min on ice to prepare the nuclei. Immediately after lysis, the nuclei were spun to remove the supernatant. The nuclei were then incubated with the Tn5 transposome and tagmentation buffer at 37 °C for 30 min (Vazyme, China). After the tagmentation, the stop buffer was directly added to the reaction to end the tagmentation. PCR was performed to amplify the library in 12 cycles. After the PCR reaction, the libraries were purified with 1.2× AMPure beads (Beckman, Germany). The libraries were sequenced using an Illumina HiSeq 2500 sequencer.The removal of the adapter sequences and mapping were performed as described for the ChIP-seq library construction and data analysis. The ATAC-seq peaks were called by MACS2 using the default parameters. All peaks are listed in GEO data set mentioned below. The peak comparisons were performed as described for the ChIP-seq library construction and data analysis. To identify the sequence motif enriched in the ATAC-seq peaks, findMotifsGenome.pl in the HOMER program was used. AnnotatePeaks.pl was used to identify specific peaks that contain certain motifs. A GREAT analysis of the ATAC-seq peaks was performed as previously described. The GREAT results are shown in Supplementary File . […]

Pipeline specifications

Software tools MACS, HOMER
Application ATAC-seq analysis
Diseases Leukemia, Neoplasms
Chemicals Tretinoin