ATAC-seq Protocol for Chromatin Profiling

ATAC-seq was carried out as described earlier with minor modification (Buenrostro et al., 2013 (link)). Cells were scraped and counted to achieve 50k/ml in ice-cold PBS. Cell suspension was further diluted to 25k/ml and nuclei were isolated with ATAC-LB (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL). Nuclei from 25k cells were used for tagmentation using Nextera DNA Library Preparation Kit (Illumina) from two biological replicates. After tagmentation DNA was purified with Minelute PCR Purification Kit (QIAGEN). Tagmented DNA was amplified with Kapa Hifi Hot Start Kit (Kapa Biosystems) using 9 PCR cycle. Amplified libraries were purified again with Minelute PCR Purification Kit. Fragment distribution of libraries was assessed with Agilent Bioanalyzer and libraries were sequenced on a HiSeq 2500 platform.

Free full text: Click here

Czimmerer Z., Daniel B., Horvath A., Rückerl D., Nagy G., Kiss M., Peloquin M., Budai M.M., Cuaranta-Monroy I., Simandi Z., Steiner L., Nagy B J.r., Poliska S., Banko C., Bacso Z., Schulman I.G., Sauer S., Deleuze J.F., Allen J.E., Benko S, & Nagy L. (2018). The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages. Immunity, 48(1), 75-90.e6.

Publication 2018

Nextera DNA Library Preparation Kit Minelute PCR Purification Kit Kapa Hifi Hot Start Kit

Atac Atac seq Biological Cell Cells nuclei Cold Dna library Mgcl2 Nacl Tris

Corresponding Organization : Sanford Burnham Prebys Medical Discovery Institute

Other organizations : University of Manchester, UD-GenoMed (Hungary), University of Virginia, Max Planck Institute for Molecular Genetics, Max Delbrück Center, University of Würzburg, Genoscope, Commissariat à l'Énergie Atomique et aux Énergies Alternatives

Top 5 similar protocols

Variable analysis

independent variables

Cells were scraped and counted to achieve 50k/ml in ice-cold PBS.
Cell suspension was further diluted to 25k/ml.
Nuclei from 25k cells were used for tagmentation.

dependent variables

Fragment distribution of libraries was assessed with Agilent Bioanalyzer.
Libraries were sequenced on a HiSeq 2500 platform.

control variables

ATAC-LB (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL) was used for nuclei isolation.
Nextera DNA Library Preparation Kit (Illumina) was used for tagmentation.
Kapa Hifi Hot Start Kit (Kapa Biosystems) was used for PCR amplification.
Minelute PCR Purification Kit (QIAGEN) was used for DNA purification.

controls

Positive control: Not mentioned.
Negative control: Not mentioned.

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!