Lutz Frönicke
@dnatech-lutz.bsky.social
DNA Technologies Core director at UC Davis.
In to everything sequencing & omics, Blechkuchen & cycling.
In to everything sequencing & omics, Blechkuchen & cycling.
"Expansion in situ sequencing" on the Aviti24 should be even wilder.
Just published, expansion in situ genome sequencing, where you can sequence DNA while still inside the cell, mapping its organization relative to proteins and other markers, with the help of expansion microscopy! Led by @jbuenrostro.bksy.social. www.science.org/doi/10.1126/...
May 30, 2025 at 9:28 PM
"Expansion in situ sequencing" on the Aviti24 should be even wilder.
Metagenome sequencing: Soil is wild indeed.
New preprint: we sequenced one soil sample with ultra-deep hybrid metagenomics and found…
→ 800+ MAGs
→ 11,000+ BGCs
→ and still nowhere near saturation.
Soil is wild.
Preprint here: www.biorxiv.org/content/10.1...
#microbiome #metagenomics #BGCs #naturalproducts #secmet
→ 800+ MAGs
→ 11,000+ BGCs
→ and still nowhere near saturation.
Soil is wild.
Preprint here: www.biorxiv.org/content/10.1...
#microbiome #metagenomics #BGCs #naturalproducts #secmet
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes
Background Soil ecosystems have long been recognized as hotspots of microbial diversity, but most estimates of their complexity remain speculative, relying on limited data and extrapolation from shall...
www.biorxiv.org
May 30, 2025 at 9:23 PM
Metagenome sequencing: Soil is wild indeed.
Reposted by Lutz Frönicke
Roche has finally given their upcoming DNA sequencer a name - Axelios. So now we can stop calling it "Genia + Stratos".
www.genomeweb.com/molecular-di...
www.genomeweb.com/molecular-di...
Roche Highlights New Tests, Instrument Launches at Investor Day
The firm touted new assays, provided an update on its nanopore sequencer, and offered insights into upcoming pipeline launches.
www.genomeweb.com
May 29, 2025 at 5:37 AM
Roche has finally given their upcoming DNA sequencer a name - Axelios. So now we can stop calling it "Genia + Stratos".
www.genomeweb.com/molecular-di...
www.genomeweb.com/molecular-di...
Reposted by Lutz Frönicke
Focus your research on specific genes with #PacBio Targeted #HiFisequencing! Get cost-effective, scalable insights for tricky regions, accurate variants & phased haplotypes. Learn about PureTarget, HiFi Target Enrichment & PCR Amplicons.
Watch now: bit.ly/3Het9pD
#PrecisionWithHiFi
Watch now: bit.ly/3Het9pD
#PrecisionWithHiFi
May 29, 2025 at 4:16 PM
Focus your research on specific genes with #PacBio Targeted #HiFisequencing! Get cost-effective, scalable insights for tricky regions, accurate variants & phased haplotypes. Learn about PureTarget, HiFi Target Enrichment & PCR Amplicons.
Watch now: bit.ly/3Het9pD
#PrecisionWithHiFi
Watch now: bit.ly/3Het9pD
#PrecisionWithHiFi
Reposted by Lutz Frönicke
Now in Nature Methods: www.nature.com/articles/s41...
See @isidrolauscher.bsky.social's explainer bsky.app/profile/isid...
See @isidrolauscher.bsky.social's explainer bsky.app/profile/isid...
May 29, 2025 at 8:07 PM
Now in Nature Methods: www.nature.com/articles/s41...
See @isidrolauscher.bsky.social's explainer bsky.app/profile/isid...
See @isidrolauscher.bsky.social's explainer bsky.app/profile/isid...
A new comparative study of commercial single-cell RNAseq kits/chemistries from the Fred Hutchinson Cancer Center: They compared seven whole transcriptome kits and three TCR kits.
scRNA-seq
www.biorxiv.org/content/10.1...
scRNA-seq
www.biorxiv.org/content/10.1...
Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies
The rapid development of updated and new commercially available single-cell transcriptomics platforms provides users with a range of experimental options. Cost, sensitivity, throughput, flexibility, a...
www.biorxiv.org
May 27, 2025 at 4:56 PM
A new comparative study of commercial single-cell RNAseq kits/chemistries from the Fred Hutchinson Cancer Center: They compared seven whole transcriptome kits and three TCR kits.
scRNA-seq
www.biorxiv.org/content/10.1...
scRNA-seq
www.biorxiv.org/content/10.1...
Reposted by Lutz Frönicke
Trying a slightly new model (for us at least) of #openscience. With @ronanchaligne.bsky.social and @karolisk.bsky.social, we pitted 10x Genomics Chromium GEM-X against Illumina PIPseq V head-to-head to understand these two platforms for single-cell genomics. Some thoughts off the bleeding edge: /1
a baby is eating a piece of food while sitting on the ground .
ALT: a baby is eating a piece of food while sitting on the ground .
media.tenor.com
March 14, 2025 at 1:29 PM
Trying a slightly new model (for us at least) of #openscience. With @ronanchaligne.bsky.social and @karolisk.bsky.social, we pitted 10x Genomics Chromium GEM-X against Illumina PIPseq V head-to-head to understand these two platforms for single-cell genomics. Some thoughts off the bleeding edge: /1
Great turnout at the "Stand Up For Science" event in Sacramento today.
March 7, 2025 at 10:02 PM
Great turnout at the "Stand Up For Science" event in Sacramento today.
Reposted by Lutz Frönicke
Yay! Paper accepted!
I still love this figure. Submitting revisions this week. SNPs in transcription factor binding sites (green) explain the majority of additive genetic variation for >70% of ~150 phenotypes (rows) in maize. See Alt for detailed figure legend. See www.biorxiv.org/content/10.1... for more!
January 31, 2025 at 2:36 PM
Yay! Paper accepted!
It looks like TWO nanopore sequencers will be announced next month.
Both are based on the "Genia" concept of sequencing labeled cDNA on silicon chip nanopores.
1) Roche promises ultra-high-throughput sequencing of short/medium-length samples at a webinar on February 20th: shorturl.at/9cjOG
1/2
Both are based on the "Genia" concept of sequencing labeled cDNA on silicon chip nanopores.
1) Roche promises ultra-high-throughput sequencing of short/medium-length samples at a webinar on February 20th: shorturl.at/9cjOG
1/2
Sequencing Platform Technologies | Nanopore sequencing
Learn about this novel nanopore-based technology using semi-conductor based electronic sensor technology to identify unique DNA bases.
shorturl.at
January 30, 2025 at 7:02 PM
It looks like TWO nanopore sequencers will be announced next month.
Both are based on the "Genia" concept of sequencing labeled cDNA on silicon chip nanopores.
1) Roche promises ultra-high-throughput sequencing of short/medium-length samples at a webinar on February 20th: shorturl.at/9cjOG
1/2
Both are based on the "Genia" concept of sequencing labeled cDNA on silicon chip nanopores.
1) Roche promises ultra-high-throughput sequencing of short/medium-length samples at a webinar on February 20th: shorturl.at/9cjOG
1/2
Microbial single-cell RNA-seq, now also for difficult samples:
"BaSSSh-seq captures extensive transcriptional heterogeneity during biofilm compared to planktonic growth."
Since the protocol uses split-pool barcoding, it can be relatively affordable.
www.nature.com/articles/s41...
"BaSSSh-seq captures extensive transcriptional heterogeneity during biofilm compared to planktonic growth."
Since the protocol uses split-pool barcoding, it can be relatively affordable.
www.nature.com/articles/s41...
Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure - Nature Communications
Microbial biofilms contain subpopulations of cells that display metabolic and transcriptional diversity. Here, Korshoj & Kielian present an optimized bacterial single-cell RNA sequencing method an...
www.nature.com
November 28, 2024 at 12:21 AM
Microbial single-cell RNA-seq, now also for difficult samples:
"BaSSSh-seq captures extensive transcriptional heterogeneity during biofilm compared to planktonic growth."
Since the protocol uses split-pool barcoding, it can be relatively affordable.
www.nature.com/articles/s41...
"BaSSSh-seq captures extensive transcriptional heterogeneity during biofilm compared to planktonic growth."
Since the protocol uses split-pool barcoding, it can be relatively affordable.
www.nature.com/articles/s41...
Reposted by Lutz Frönicke
Our lab's latest preprint investigates the dynamic RNA modification landscape in the #liverwort Riccia fluitans during its transition from a terrestrial to an aquatic environment. We employed @nanoporetech.com DRS for the identification and validation (adapted PRAISE metod) these modifications.
Unlocking the Secrets of Amphibious Plant Adaptation: The Role of RNA Modifications https://www.biorxiv.org/content/10.1101/2024.11.25.625166v1
Unlocking the Secrets of Amphibious Plant Adaptation: The Role of RNA Modifications https://www.biorxiv.org/content/10.1101/2024.11.25.625166v1
Post-transcriptional RNA modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), an
www.biorxiv.org
November 27, 2024 at 4:58 AM
Our lab's latest preprint investigates the dynamic RNA modification landscape in the #liverwort Riccia fluitans during its transition from a terrestrial to an aquatic environment. We employed @nanoporetech.com DRS for the identification and validation (adapted PRAISE metod) these modifications.
Reposted by Lutz Frönicke
New method out for structural variants studies called Kanpig. Huge improvements on tandem repeat regions where 70% of sv are. Great new method from Adam English!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 26, 2024 at 5:29 PM
New method out for structural variants studies called Kanpig. Huge improvements on tandem repeat regions where 70% of sv are. Great new method from Adam English!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...