Qiagen's Parse Biosciences Deal Marks New Era of Competition for Single-Cell Techs www.genomeweb.com/sequencing/q...
07.11.2025 20:31
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Qiagen's Parse Biosciences Deal Marks New Era of Competition for Single-Cell Techs www.genomeweb.com/sequencing/q...
Full house @10xgenomics.bsky.social user day! People didn’t come because of the bagels ( as there are still some left) but for technology 😂 @fgcz-en.bsky.social
🧬 Meet our #Genomics Unit!
Led by @catharineaquino.bsky.social, our team specializes in #ngs, #single-cell transcriptomics, #spatial gene expression, #long-read sequencing & genome engineering. From DNA to RNA to protein to metabolites!
Video 🔗 learn more about our services: tinyurl.com/zemh8bsy
Big thanks to Monica Manotas for visiting the @fgcz-en.bsky.social in your very first week as CEO of Tecan. Nothing like jumping straight into customer visits (starting with the nicest customer, of course 😇 ) and what a fantastic way to kick off the new role!
🔬Ever wondered what goes on inside one of Switzerland's leading #omics core facilities? Join us for an exclusive behind-the-scenes tour of the Functional Genomics Center Zurich! Supporting researchers from @ethz.ch, UZH, and beyond across #genomics, #proteomics & #metabolomics.
🔗 fgcz.ch
Hmm, was it really in a lower level before? 🫣
PS. We really do receive your samples with a smile, especially if they’re properly labeled 😀
Massive thanks to the dream team behind the Genomics Unit, both on screen and behind the scenes. From next-gen sequencing to spatial transcriptomics to CRISPR, we’ve got you covered with cutting-edge, state-of-the-art genomics technologies. shorturl.at/H4Oa2
The novaseqx? 😇
Swiss Genome of the 1918 Influenza Virus Reconstructed!
So proud of @fgcz-en.bsky.social Genomics Unit’s Spatial Expert,Christian Urban,for authoring such a cool paper!Nothing like cool science+great storytelling! Of course,part of the sequencing was done at the FGCZ
www.news.uzh.ch/en/articles/...
Take a peek inside our @fgcz-en.bsky.social . Watching the video, I’m struck by how neat, clean, and sci-fi labglam it is. I can confirm it really does look like that IRL. We didn’t tidy up just for the video and we really wear lab coats 😄
oc-aem-dist-downloads.ethz.ch/mh_default_o...
Because our resources are limited. We can’t afford to offer a protocol without an added value to our portfolio hence the benchmarking before offering it.
Verdict:
If your study hinges on squeezing out every cell, go with GEMX. But if you are balancing budget and performance, PIPseq might be something to consider. We now added PIPseq to our services.
Bottom line
GEMX has the edge in cell detection, but PIPseq performs respectably at roughly half the price. For many experiments, that trade off could be worth it.
Gene Expression
Very close. Both platforms delivered comparable gene detection per cell and high transcriptome mapping rates. Both platforms found the same cell types.
Cell Detection
GEMX detected significantly more cells (24,339 vs 15,324) average cells using Empty Drops on all samples for fair cell calling comparison, indicating higher sensitivity in cell calling.
A Promising Single Cell Alternative
Before we roll out any new service, internal benchmarking is a must. This time we tested Illumina’s Single Cell 3' RNA prep kit (which I will call PIPseq) against the reigning champ, 10x Genomics GEMX 3' Gene Expression kit (GEMX for short).
What we found:
Great to have Duncan Yu of MGI swing by the @fgcz-en.bsky.social ! It’s always a pleasure when genomics powerhouses come bearing insights. Of course , we did the required photo op in front of our building artwork 😆 😀
I didn’t dare try to go!
If you're at #ASMS2025, check out the posters from our @fgcz-en.bsky.social #Proteomics colleagues, especially the one on NGS-based proteomics that the #Genomics and #Bioinformatics units had the pleasure of contributing to 😊. @paolonanni.bsky.social TobiasKockmann @hubertr.bsky.social ClaudiaFortes
The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers. #RNAseq #PCRduplication #Benchmarking #Genomics #GenomeBiology
genomebiology.biomedcentral.com/articles/10....
Thanks! I didn’t realize I copied the link from linkedin when I copied the post .
🧬 New study in Gen. Bio.! We tested how RNA input & PCR cycles affect duplication rates across 4 sequencers. ↘️ RNA = ↗️ duplicates = ↘️ diversity. Key for optimizing RNA-seq protocols! Thanks + congrats to @catharineaquino.bsky.social @nataliazajac.bsky.social + collaborators!
🔗 tinyurl.com/bdcuen59
This study was a collaborative effort with contributions from Natalia Zajac, Ioannis S. Vlachos, Sija Sajibu, Lennart Opitz, Shuoshuo Wang, Sridar V. Chittur, Christopher E. Mason, Kevin L. Knudtson, John M. Ashton, Hubert Rehrauer, Catharine Aquino, and others.
These insights are crucial for optimizing RNA-seq library preparation protocols, especially when working with limited RNA quantities.
We evaluated RNA input amts and PCR cycles affect PCR dups rates in 4 platforms: NS6000, NovaseqX, Element AVITI, and Singular G4. We saw that lower RNA inputs and higher PCR cycles increase dups , leading to reduced read diversity, fewer detected genes, and increased noise in expression counts.
I’m very happy to share our latest ABRF - Genomics ResearchGroup study “The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers,” is now published in Genome Biology!
genomebiology.biomedcentral.com/articles/10....
The yearly Core4Life Genomics meeting is my favorite of the year. 8 great EU cores meet to swap secrets, voodoos & hacks on running genomics tech. This year was hosted by Vladimir Benes and Laura Villacorta @EMBL. The vibe: a platform-agnostic space where tech diversity isn’t a bug , it’s a feature.
