AutoRELACS: Automated Generation And Analysis of Ultra-parallel ChIP-seq

We present AutoRELACS, an automated implementation of the RELACS protocol using the Biomek i7 automated workstation (Beckman&Coulter). We test the performance of AutoRELACS by assessing 1) the scalability of the chromatin barcode integration step, 2) the quality of the generated data in comparison to the benchmark set by the manual protocol, and 3) the sensitivity of the automated method when working with low (≤ 25.000 cells/sample) and very low (≤ 5.000 cells/sample) cell numbers. 1) First, we test the effciency of automated barcode integration. We barcode 60 batches of S2 cells and we sequence only the input chromatin. 2) To test the overall quality of AutoRELACS in comparison to the manual protocol, we barcode the chromatin of 28 batches of S2 cells using custom RELACS adaptors and we pool them together using Biomek i7 automated workstation. The chromatin is used to generate genome-wide profiles for H3K4me3, H3K27ac and H3K27me3. 3) To test the sensitivity of the automated RELACS protocol, we profile the same three histone marks using 4 batches of HepG2 cells. We distribute the barcoded cells into two poolings. The Low pool contained a total of 300,000 cells, while the Very Low pool contained a total of 60,000 cells (see Fig 3a of publication for details).