6 Articles found

AtlasXomics Inc. articles

Spatial profiling of chromatin accessibility in mouse and human tissues

Abstract

Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context¹. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping

Aug. 17, 2022

Yanxiang Deng;Marek Bartosovic;Sai Ma;Di Zhang;Petra Kukanja;Yang Xiao;Graham Su;Yang Liu;Xiaoyu Qin;Gorazd B. Rosoklija;Andrew J. Dwork;J. John Mann;Mina L. Xu;Stephanie Halene;Joseph E. Craft

Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level

Close-up on chromatin modifications

Despite recent advances in spatial transcriptomics to map gene expression, it has not be possible to determine the underlying epigenetic mechanisms controlling gene expression and tissue development with high spatial resolution. Denget al. report on a technique called spatial-CUT&Tag for genome-wide profiling of histone modifications pixel by pixel on a frozen tissue section without

Feb. 9, 2022

Yanxiang Deng;Petra Kukanja;Marek Bartosovic;Di Zhang;Yang Liu;Graham Su;Archibald Enninful;Zhiliang Bai;Gonçalo Castelo-Branco;Rong Fan

Seven technologies to watch in 2022

Our fifth annual round-up of the tools that look set to shake up science this year.

From gene editing to protein-structure determination to quantum computing, here are seven technologies that are likely to have an impact on science in the year ahead.

Fully finished genomes

Roughly one-tenth of the human genome remained uncharted when genomics researchers Karen Miga at the University of California, Santa Cruz, and Adam Phillippy at the National

Jan. 25, 2022

Michael Eisenstein

Spatial multi-omics sequencing for fixed tissue via DBiT-seq

Highlights

Simultaneous transcriptomic and proteomic analysis on fixed tissue slides
10- and 25-μm spot size for varying resolution and near-single-cell analysis
DBiT-seq can be conducted with common laboratory equipment and reagents
DBiT-seq produces high-quality RNA sequencing data with high spatial resolution (10 μm)

Summary

This protocol describes the use of the determini

Jun. 18, 2021

Graham Su;Xiaoyu Qin;Archibald Enninful;Zhiliang Bai;Yanxiang Deng;Yang Liu;Rong Fan

Multiomics sequencing goes spatial

Microfluidic channels provide a means to deliver barcodes encoding spatial information to a tissue, which allows co-profiling of gene expression and proteins of interest in a spatially resolved manner.

Back in 2013, Rong Fan from Yale University was intrigued by a conversation with colleague Kathryn Miller-Jensen: they noticed that trypsinizing cancer cells off the substrate could perturb the measurements of the signaling network. Since then, Fan has been thinking about how to fix

Jan. 6, 2021

Lei Tang