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Catharine.Aquino @catharineaquino.bsky.social · 28d

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

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Reposted by Catharine.Aquino

Functional Genomics Center Zurich @fgcz-en.bsky.social · Aug 11

🧬 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

tinyurl.com

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Catharine.Aquino @catharineaquino.bsky.social · Aug 7

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!

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Reposted by Catharine.Aquino

Functional Genomics Center Zurich @fgcz-en.bsky.social · Aug 6

🔬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

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Catharine.Aquino @catharineaquino.bsky.social · Aug 6

Hmm, was it really in a lower level before? 🫣

PacBio @pacbio.bsky.social · Jul 31

European genomics is leveling up, thanks to Dr. Ibrahim Bitar’s work with #Vega in the Czech Republic.
📖 Read his story: bit.ly/3Jda9sg
#HiFiSequencing #TheresHiFiForThat

Customer success story: How Dr. Ibrahim Bitar is doubling his research impact while leading the future of European genomics from the Czech Republic - PacBio

Dr. Bitar is a true champion of innovation, bringing PacBio HiFi sequencing to some of the most difficult-to-sequence samples.

bit.ly

Catharine.Aquino @catharineaquino.bsky.social · Aug 5

PS. We really do receive your samples with a smile, especially if they’re properly labeled 😀

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Catharine.Aquino @catharineaquino.bsky.social · Aug 5

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

Follow our video series spotlighting the different omics units at our center. | Functional Genomics Center Zurich

Follow our video series spotlighting the different omics units at our center. This week, we first meet the Genomics Unit, following the central dogma from DNA to RNA to protein to metabolites. The uni...

www.linkedin.com

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Catharine.Aquino @catharineaquino.bsky.social · Jul 31

The novaseqx? 😇

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Catharine.Aquino @catharineaquino.bsky.social · Jul 31

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/...

Swiss Genome of the 1918 Influenza Virus Reconstructed

www.news.uzh.ch

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Catharine.Aquino @catharineaquino.bsky.social · Jul 29

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...

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Catharine.Aquino @catharineaquino.bsky.social · Jul 28

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.

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Catharine.Aquino @catharineaquino.bsky.social · Jul 27

Full post here : www.linkedin.com/posts/cathar...

A Promising Single Cell Alternative | Catharine Aquino

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 t...

www.linkedin.com

Catharine.Aquino @catharineaquino.bsky.social · Jul 27

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.

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Catharine.Aquino @catharineaquino.bsky.social · Jul 27

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.

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Catharine.Aquino @catharineaquino.bsky.social · Jul 27

Gene Expression
Very close. Both platforms delivered comparable gene detection per cell and high transcriptome mapping rates. Both platforms found the same cell types.

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Catharine.Aquino @catharineaquino.bsky.social · Jul 27

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.

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Catharine.Aquino @catharineaquino.bsky.social · Jul 27

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:

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Catharine.Aquino @catharineaquino.bsky.social · Jun 6

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 😆 😀

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Catharine.Aquino @catharineaquino.bsky.social · Jun 3

I didn’t dare try to go!

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Catharine.Aquino @catharineaquino.bsky.social · Jun 3

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

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Reposted by Catharine.Aquino

Javier Santoyo @jsantoyo.bsky.social · Jun 3

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....

The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers - Genome Biology

Background Transcriptome sequencing (RNA-seq) is a powerful technology for gene expression profiling. Selection of optimal parameters for cDNA library generation is crucial for acquisition of…

genomebiology.biomedcentral.com

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Catharine.Aquino @catharineaquino.bsky.social · May 28

Thanks! I didn’t realize I copied the link from linkedin when I copied the post .

Reposted by Catharine.Aquino

Functional Genomics Center Zurich @fgcz-en.bsky.social · May 28

🧬 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

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Catharine.Aquino @catharineaquino.bsky.social · May 28

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.