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1. Methylomes and transcriptomes raw data are processed using in-house pipelines (WGBS pipeline showed) 2. The processed data are grouped based on the origin and environments 3. Using PostgreSQL to store the data 4. Using Django to set up web browser for #DME #SVCRS2021 (2/5)

Currently, the #DME database includes >11500 methylomes and >1600 matched sample transcriptomes covered 20 cancer types and 11 non-cancer diseases. Provided features include originally invested samples, clinical-pathological data. #SVCRS2021 (3/5)

#DME is equipped with a user-friendly interface for searching and visualization Non-overlap DMCs between cancers provides CpG candidates for biomarker discovery ZNF154 locus are described to be differentially methylated in many cancers that could be validated #SVCRS2021 (4/5)

The #DME database enables biologists to perform analyses regarding DNA methylation alterations in public data. Database will provide a valued resource for the community and may be used to aid cancer methylation biomarker discovery and validation studies. #SVCRS2021 (5/5)

Nice summary!

Our next Center for Integrated Cellular Analysis virtual seminar is Nov 16 at 12PM EST. Bingjie Zhang and Avi Srivastava will introduce scCUT&Tag-pro and scChromHMM - tools to measure, integrate, and analyze histone modification profiles in single cells. Free registration at: nygenome.zoom.us/meeting/regist…

Save the date! AEpiA Epigenetics Conference is back, 11-14 Sept 2022, for a face to face meeting in Kingscliff NSW. Registration and abstracts will open early 2022 #AusEpi22

Our Chromap paper is published today, so people can use this instead of BWA for ChIP-seq, HiC, scATAC-seq alignment and pre-processing. This should be cited more than MACS!

I love this tool :D

Good move! science.org/content/articl…

Nice lecture!

Job

Interested in single cell genomics but need help getting started? Check out the full agenda for our Single Cell Genomics Day next Friday (3/4). All talks will be live-streamed (no registration required) at satijalab.org/scgd22

Out today - DNA methylation alterations in metabolic, inflammatory, and cholesterol pathways associated with ALS science.org/doi/10.1126/sc…. Huge collaborative effort led by Paul Hop and ramona zwamborn. Project MinE Exeter Med School University of Exeter News

Study of the effects of forcing DNA methylation using zinc finger-DNMT3A fusion protein, from Alex de Mendoza, Trung Nguyen, Ford, ryan lister & co. Effects on transcription are context-dependent, including upregulation, and the methylation is lost rapidly genomebiology.biomedcentral.com/articles/10.11…

Yes, it is!

Pangene is a new tool for constructing a pangenome gene graph from multiple assemblies: github.com/lh3/pangene. You can explore the rich haplotypic diversity of human genes at pangene.liheng.org. Still WIP.

Terrifying plot for those working in microbiome profiling

Great to see this recent article in Nature Cell Biology nature.com/articles/s4155… complements our work in NatureStructMolBiol nature.com/articles/s4159… showing LINE1 functioning as enhancers