Project description:The submitted files contain ChIP-seq data for the p300 transcriptional coactivator in GM12878 cells and for the NRSF transcription factor in GM12878 and Jurkat cells generated using a fully automated robotic chromatin immunoprecipitation protocol. Cells were fixed using 1% formaldehyde (NRSF samples) or 1% formaldehyde at 37C (p300 samples).
Project description:Setup and optimisation of a high throughput pipeline for ChIPseq. The protocol used is ChIP carried out using the Agilent Bravo robot with subsequent Ilumina sequencing library preparation.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Project description:Samples were generated by mixing commercially available tryptic digests (human: K562, HeLa; yeast (S.cerevisiae); E.coli) in defined proportions, to create a dataset with known ground truth, for benchmarking of the quantitative performance and scalability of DIA raw data processing software. Acquisition was performed in high throughput using the Evosep One system operated in microflow mode coupled to Bruker timsTOF Ultra in dia-PASEF mode. The experiment design is specified in the “Experiment_design.xlsx” file attached and achieves the following: - The human background is perturbed in a controlled manner, by mixing K562 and HeLa digests in defined proportions, to model the biological variation observed in applications. The E.coli digest within the samples serves for normalisation, whereas the yeast digest is added in different proportions relative to E.coli in different samples and therefore allows the evaluate the quantitative accuracy of the method. - The scale of the experiment allows to evaluate the effect of the number of samples on the quantitative performance of the software. - The experiment involves acquisitions with medium-high to very low load, modelling the rapidly emerging applications of high-sensitivity DIA proteomics.
Project description:Recent advances in stem cell technology have led to the development of three-dimensional (3D) culture systems called organoids, which have fueled hopes to bring about the next generation of more physiologically relevant high throughput screens (HTS). However, the adaptation of established organoid protocols for HTS applications has so far been elusive. Here, we present a fully scalable, HTS-compatible workflow for the automated generation, maintenance, whole mount staining, clearing, and optical analysis of human neural organoids generated from neural precursor cells in a standard 96-well format. By combining organoid generation and analysis steps in an automated fashion, we can perform quantitative whole-organoid high content imaging with single cell resolution. The resulting organoids are highly homogeneous with regard to their morphology, size, global gene expression, cellular composition, and structure. Calcium imaging suggests organoid-wide synchronized functional coupling. The scalability of our approach has the potential to form the basis for 3D tissue-based screening in a variety of applications including drug development, toxicology studies, and disease modeling.