Super excited to share the first application of #FixNCut! A fantastic collaboration with Sahar Nissim and his dream team from ⁦Brigham and Women's Hospital⁩ | ⁦Dana-Farber⁩ Adelaide Centre for Epigenetics Uni of Adelaide South Australian immunoGENomics Cancer Institute ⁦Gastroenterology⁩ gastrojournal.org/article/S0016-…

If you are attending #abrf2024 don’t miss our talk about The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI and G4 sequencers Tues3pm.See you ! Natalia Zajac Ioannis Vlachos Sridar Chittur John Ashton Illumina Element Biosciences Singular Genomics

Presentation done #abrf2024 . Please find the preprint here biorxiv.org/content/10.110… most of the figures we presented can be found there.

Molecular Pixelation!! An optics-free, DNA sequence-based method for spatial proteomics of single cells using antibody–oligonucleotide conjugates (AOCs) and DNA-based, nanometer-sized molecular pixels. nature.com/articles/s4159…

Pathology job postings up 2x+ since 2017 meridian.allenpress.com/aplm/article/1… From tissuepathology

1/6 Introducing MultiMIL: a weekly supervised multimodal model to identify disease-specific changes in single-cell atlases. Using a multiple-instance learning framework and attention mechanism, it prioritizes cells linked to various phenotypes in a large single-cell reference

Step by step guide of a life changing single cell protocol!

How different are single cell quantification results between Cell Ranger versions? Quite different - depending on the versions - We and many other groups have done similar analyses internally with concordant results. biorxiv.org/content/10.110…

Earlier this week we carried out a preliminary analysis of our first 10x Genomics Xenium prime (5,000 gene) run. We had designed this experiment to get a sense of how the prime chemistry performed compared to the Xenium V1 chemistry.

Really elegant work! Detection of transcriptome-wide microRNA–target interactions in single cells with agoTRIBE nature.com/articles/s4158…

Making Perturb-Seq easier and efficient by linear combinations and deconvolution of the genetic perturbations Compressed Perturb-seq enables highly efficient genetic screens nature.com/articles/s4158…

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics! genomebiology.biomedcentral.com/articles/10.11…

Now out - WebAtlas pipeline for visualizing and processing integrated single cell and spatial transcriptomics data ⁦Nature Methods⁩ ⁦Omer Ali Bayraktar⁩ ⁦Haniffa Lab⁩ ⁦Shila Ghazanfar⁩ ⁦Human Cell Atlas⁩ github.com/haniffalab/web… nature.com/articles/s4159…

#spatialomics has been described as a ‘Scientific Wild West’ right now, but how do we escape it? The final chapter of our latest report explores this question and comes up with the most likely answer – community 👭👬(check out @GESTALT_SP). Download here - hubs.la/Q02M1cLv0

A personalized antisense oligonucleotide developed for a single patient was well tolerated and led to preliminary improvements in mobility and behavioural arrests in a girl with KIF1A-associated neurological disorder, after 9 months follow up. Wendy Chung nature.com/articles/s4159…

We are humbled to have our lab's work featured this week on the cover of nature (below), with many, many people to thank. First, the stellar crew of Inspiration4, Jared Isaacman, Hayley Arceneaux, Chris “Hanks” Sembroski 🇺🇦, Dr. Sian “Leo” Proctor, who donated time, blood, fluids, and sweat for

FixNCut: A Practical Guide to Sample Preservation by Reversible Fixation for Single Cell Assays bio-protocol.org/en/bpdetail?id…

Tricky timelines, logistic hurdles, sensitive samples or very difficult tissues??? Fix your cells and tissues before doing your single cell work! Awesome results every time with reversible fixation. Step by step how with FixNCut!

September 18 & October 10, 10AM EST. Don't miss the two upcoming #GESTALT meetings! shorturl.at/PPAfb

Celcomen: spatial causal disentanglement for single-cell and tissue perturbation modeling By Teichlab arxiv.org/abs/2409.05804