If you want to do single-cell RNA-seq on your favourite bacterium, here‘s our detailed Nature Protocol for microbial MATQ-seq. It profiles up to 600 genes in a single bacterial cell!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Transcriptomic profiling of individual bacteria by MATQ-seq - Nature Protocols
Bacterial single-cell sequencing via MATQ-seq combines index sorting, random priming and rRNA depletion, and offers high cell retention and transcript capture rates, making it ideal for experiments wi...
www.nature.com
April 9, 2025 at 9:15 AM
If you want to do single-cell RNA-seq on your favourite bacterium, here‘s our detailed Nature Protocol for microbial MATQ-seq. It profiles up to 600 genes in a single bacterial cell!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Excited to share: enhanced capture in vivo multiome Perturb-seq!
Worried about low gRNA recovery and wasting sequencing on cells that can’t assign a perturbation? We engineered gRNA transcripts to stay in the nucleus, enabling efficient multiomic Perturb-seq!
www.biorxiv.org/content/10.6...
Worried about low gRNA recovery and wasting sequencing on cells that can’t assign a perturbation? We engineered gRNA transcripts to stay in the nucleus, enabling efficient multiomic Perturb-seq!
www.biorxiv.org/content/10.6...
March 17, 2026 at 1:23 PM
Excited to share: enhanced capture in vivo multiome Perturb-seq!
Worried about low gRNA recovery and wasting sequencing on cells that can’t assign a perturbation? We engineered gRNA transcripts to stay in the nucleus, enabling efficient multiomic Perturb-seq!
www.biorxiv.org/content/10.6...
Worried about low gRNA recovery and wasting sequencing on cells that can’t assign a perturbation? We engineered gRNA transcripts to stay in the nucleus, enabling efficient multiomic Perturb-seq!
www.biorxiv.org/content/10.6...
New preprint from our lab!
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
September 19, 2025 at 3:03 AM
New preprint from our lab!
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
High-throughput capture of transcription factor-driven epigenome dynamics using PHILO ChIP-seq academic.oup.com/nar/advance-...
From Mark Zander lab!
From Mark Zander lab!
High-throughput capture of transcription factor-driven epigenome dynamics using PHILO ChIP-seq
Abstract. Assessing the dynamics of chromatin features and transcription factor (TF) binding at scale remains a significant challenge in plants. Here, we p
academic.oup.com
December 3, 2024 at 10:42 PM
High-throughput capture of transcription factor-driven epigenome dynamics using PHILO ChIP-seq academic.oup.com/nar/advance-...
From Mark Zander lab!
From Mark Zander lab!
Stereo-seq V2 facilitates single-cell-resolution spatial RNA mapping in FFPE samples through random primer capture, uncovering ncRNAs, host-pathogen transcriptome profiling, and spatial immune repertoires in situ @cellcellpress.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
August 28, 2025 at 10:08 PM
Stereo-seq V2 facilitates single-cell-resolution spatial RNA mapping in FFPE samples through random primer capture, uncovering ncRNAs, host-pathogen transcriptome profiling, and spatial immune repertoires in situ @cellcellpress.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Different approaches to preparing and sequencing bacterial RNA libraries capture comparable transcriptional profiles:
journals.asm.org/doi/10.1128/...
#microsky #PsWatch #bacteria
journals.asm.org/doi/10.1128/...
#microsky #PsWatch #bacteria
RNA-seq reproducibility of Pseudomonas aeruginosa in laboratory models of cystic fibrosis | Microbiology Spectrum
RNA sequencing (RNA-seq) has revolutionized biology, but many steps in RNA-seq workflows
can introduce variance, potentially compromising reproducibility. While reproducibility
in RNA-seq has been tho...
journals.asm.org
December 5, 2024 at 11:07 PM
Different approaches to preparing and sequencing bacterial RNA libraries capture comparable transcriptional profiles:
journals.asm.org/doi/10.1128/...
#microsky #PsWatch #bacteria
journals.asm.org/doi/10.1128/...
#microsky #PsWatch #bacteria
Gene fusions drive ~16% of all cancers & 50-70% of childhood ALL. But standard scRNA-seq can't see them — the assays aren't built to capture fusion breakpoints. We built a way to fix that. @aliciao.bsky.social @sadras-t.bsky.social @petermaccc.bsky.social @onjcri.org.au @10xgenomics.bsky.social 🧵
Closing the fusion-detection gap in single-cell RNA-seq with a scalable, probe-based workflow https://www.biorxiv.org/content/10.64898/2026.08.26.747171v1
August 31, 2026 at 1:40 AM
Gene fusions drive ~16% of all cancers & 50-70% of childhood ALL. But standard scRNA-seq can't see them — the assays aren't built to capture fusion breakpoints. We built a way to fix that. @aliciao.bsky.social @sadras-t.bsky.social @petermaccc.bsky.social @onjcri.org.au @10xgenomics.bsky.social 🧵
These variants capture deleterious regulatory variation that selection would otherwise purge. A TNRC18 intronic variant (115x in Finns) raises IBD risk and lowers TNRC18 in T cells. Base editing (STAG-seq) confirmed it and revealed retroviral reactivation: doi.org/10.1101/2025...
September 30, 2026 at 5:27 PM
These variants capture deleterious regulatory variation that selection would otherwise purge. A TNRC18 intronic variant (115x in Finns) raises IBD risk and lowers TNRC18 in T cells. Base editing (STAG-seq) confirmed it and revealed retroviral reactivation: doi.org/10.1101/2025...
New Article! Transcriptomic profiling of individual bacteria by MATQ-seq
Transcriptomic profiling of individual bacteria by MATQ-seq
Nature Protocols, Published online: 09 April 2025; doi:10.1038/s41596-025-01157-5Bacterial single-cell sequencing via MATQ-seq combines index sorting, random priming and rRNA depletion, and offers high cell retention and transcript capture rates, making it ideal for experiments with limited starting material.
bit.ly
April 9, 2025 at 9:42 AM
New Article! Transcriptomic profiling of individual bacteria by MATQ-seq
A Nature study uses #PacBio long-read sequencing to map chromatin architecture in single cells with DAF-seq, extending Fiber-seq and showing multiomic HiFi reads capture chromatin features and sequence, revealing haplotype-specific regulatory variation across cells.
Details: go.nature.com/4pODNVl
Details: go.nature.com/4pODNVl
Mapping single-cell diploid chromatin fiber architectures using DAF-seq - Nature Biotechnology
Single-molecule chromatin fiber sequencing exposes single-cell-level heterogeneity in the chromatin architecture of individual regulatory elements.
https://go.nature.com/4pODNVl"
December 16, 2025 at 9:31 PM
A Nature study uses #PacBio long-read sequencing to map chromatin architecture in single cells with DAF-seq, extending Fiber-seq and showing multiomic HiFi reads capture chromatin features and sequence, revealing haplotype-specific regulatory variation across cells.
Details: go.nature.com/4pODNVl
Details: go.nature.com/4pODNVl
CINTER-seq enables in situ capture and multimodal profiling of interacting cells in living mice, uncovering specific LAG3-MHC II-mediated CD4+ T cell-cancer cell interactions & tumor-reprogrammed neutrophils
www.cell.com/immunity/ful... @cp-immunity.bsky.social
www.cell.com/immunity/ful... @cp-immunity.bsky.social
July 17, 2025 at 4:50 PM
CINTER-seq enables in situ capture and multimodal profiling of interacting cells in living mice, uncovering specific LAG3-MHC II-mediated CD4+ T cell-cancer cell interactions & tumor-reprogrammed neutrophils
www.cell.com/immunity/ful... @cp-immunity.bsky.social
www.cell.com/immunity/ful... @cp-immunity.bsky.social
Important thread.
UCLA seems to have chosen to abandon basic norms of independent thought needed for scholarship and teaching. And capitulation to a nat’l push to capture academic institutions and turn them into ideological arms of the state is…too familiar to Jews with memories of 1933 et seq.
UCLA seems to have chosen to abandon basic norms of independent thought needed for scholarship and teaching. And capitulation to a nat’l push to capture academic institutions and turn them into ideological arms of the state is…too familiar to Jews with memories of 1933 et seq.
1/ I represent 5 anti-zionist students and faculty challenging the outrageous claim that the Palestine Solidarity Encampment was a "Jew exclusion zone". UCLA refused to defend. Today they agreed to pay millions instead. I can't overstate how dangerous this is. 🧵
www.latimes.com/california/s...
www.latimes.com/california/s...
UCLA to pay $6.45 million to settle suit by Jewish students over pro-Palestinian protests
UCLA agreed to settle a lawsuit by Jewish students who alleged the university aided a 2024 pro-Palestinian encampment, which the lawsuit alleged illegally discriminated against Jewish people.
www.latimes.com
July 30, 2025 at 2:16 PM
Important thread.
UCLA seems to have chosen to abandon basic norms of independent thought needed for scholarship and teaching. And capitulation to a nat’l push to capture academic institutions and turn them into ideological arms of the state is…too familiar to Jews with memories of 1933 et seq.
UCLA seems to have chosen to abandon basic norms of independent thought needed for scholarship and teaching. And capitulation to a nat’l push to capture academic institutions and turn them into ideological arms of the state is…too familiar to Jews with memories of 1933 et seq.
Cool framework to systematically compare & evaluate methods that integrate scRNA+ATAC-seq data to infer GRNs, highlighting limitations & variability in performance across different tasks and clear challenge to capture causal relationships from perturbation assays www.biorxiv.org/content/bior...
www.biorxiv.org
December 24, 2024 at 9:18 AM
Cool framework to systematically compare & evaluate methods that integrate scRNA+ATAC-seq data to infer GRNs, highlighting limitations & variability in performance across different tasks and clear challenge to capture causal relationships from perturbation assays www.biorxiv.org/content/bior...
SenCID
a 6-module single-cell transcript feature for #Senescence
CROP-seq
Smooth muscle cell ➡️SID2
Endothelial cell ➡️SID4
Fibroblast ➡️SID5
Capture 👤Lung aging (AT2), Skin aging (fibroblast), Osteoarthritis (chondrocyte), Atherosclerosis (aortic EC)
#CellMetab 2024
www.cell.com/cell-metabol...
a 6-module single-cell transcript feature for #Senescence
CROP-seq
Smooth muscle cell ➡️SID2
Endothelial cell ➡️SID4
Fibroblast ➡️SID5
Capture 👤Lung aging (AT2), Skin aging (fibroblast), Osteoarthritis (chondrocyte), Atherosclerosis (aortic EC)
#CellMetab 2024
www.cell.com/cell-metabol...
December 22, 2025 at 1:04 PM
SenCID
a 6-module single-cell transcript feature for #Senescence
CROP-seq
Smooth muscle cell ➡️SID2
Endothelial cell ➡️SID4
Fibroblast ➡️SID5
Capture 👤Lung aging (AT2), Skin aging (fibroblast), Osteoarthritis (chondrocyte), Atherosclerosis (aortic EC)
#CellMetab 2024
www.cell.com/cell-metabol...
a 6-module single-cell transcript feature for #Senescence
CROP-seq
Smooth muscle cell ➡️SID2
Endothelial cell ➡️SID4
Fibroblast ➡️SID5
Capture 👤Lung aging (AT2), Skin aging (fibroblast), Osteoarthritis (chondrocyte), Atherosclerosis (aortic EC)
#CellMetab 2024
www.cell.com/cell-metabol...
Single-cell RNA-seq is younger than the iPhone. 🤯 The first bona fide scRNA-seq transcriptomes were published in 2009 by Tang et al., who sequenced individual mouse cells and showed you could capture a whole transcriptome from a single cell. From “sci-fi” to standard tool in just over a decade...
November 25, 2025 at 1:47 AM
Single-cell RNA-seq is younger than the iPhone. 🤯 The first bona fide scRNA-seq transcriptomes were published in 2009 by Tang et al., who sequenced individual mouse cells and showed you could capture a whole transcriptome from a single cell. From “sci-fi” to standard tool in just over a decade...
Microbial single-cell MATQ-seq developed by @emmanuel-saliba.bsky.social & @jorg-vogel-lab.bsky.social allows detection of a large number of genes per single bacterium & stands out for its high rate of cell retention.
For a detailed protocol, see rdcu.be/eg0Xc, now available @natprot.bsky.social.
For a detailed protocol, see rdcu.be/eg0Xc, now available @natprot.bsky.social.
Transcriptomic profiling of individual bacteria by MATQ-seq
Nature Protocols - Bacterial single-cell sequencing via MATQ-seq combines index sorting, random priming and rRNA depletion, and offers high cell retention and transcript capture rates, making it...
rdcu.be
April 9, 2025 at 10:56 AM
Microbial single-cell MATQ-seq developed by @emmanuel-saliba.bsky.social & @jorg-vogel-lab.bsky.social allows detection of a large number of genes per single bacterium & stands out for its high rate of cell retention.
For a detailed protocol, see rdcu.be/eg0Xc, now available @natprot.bsky.social.
For a detailed protocol, see rdcu.be/eg0Xc, now available @natprot.bsky.social.
Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution www.cell.com/cell/fulltex...
Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution
Stereo-seq V2 facilitates single-cell-resolution spatial RNA mapping in FFPE samples
through random primer capture, uncovering ncRNAs, host-pathogen transcriptome profiling,
and spatial immune reperto...
www.cell.com
September 8, 2025 at 7:56 PM
Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution www.cell.com/cell/fulltex...
📜 Best practices for the execution, analysis, and data storage of plant single- cell/nucleus transcriptomics
🧑🔬 Carolin Grones, Marc Libault, Bert De Rybel, et al.
📔 The Plant Cell
🔗 academic.oup.com/plcell/advan...
#️⃣ (Feeds) #PlantScience #PlantTranscriptomics #PlantSingleCellSeq #DataManagement
🧑🔬 Carolin Grones, Marc Libault, Bert De Rybel, et al.
📔 The Plant Cell
🔗 academic.oup.com/plcell/advan...
#️⃣ (Feeds) #PlantScience #PlantTranscriptomics #PlantSingleCellSeq #DataManagement
Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcript...
Abstract. Single-cell and single-nucleus RNA-sequencing (scRNA-seq and snRNA-seq) technologies capture the expression of plant genes at an unprecedented resolut
academic.oup.com
January 18, 2024 at 1:07 PM
📜 Best practices for the execution, analysis, and data storage of plant single- cell/nucleus transcriptomics
🧑🔬 Carolin Grones, Marc Libault, Bert De Rybel, et al.
📔 The Plant Cell
🔗 academic.oup.com/plcell/advan...
#️⃣ (Feeds) #PlantScience #PlantTranscriptomics #PlantSingleCellSeq #DataManagement
🧑🔬 Carolin Grones, Marc Libault, Bert De Rybel, et al.
📔 The Plant Cell
🔗 academic.oup.com/plcell/advan...
#️⃣ (Feeds) #PlantScience #PlantTranscriptomics #PlantSingleCellSeq #DataManagement
Using Promoter Capture Hi-C, we linked STARR-seq enhancers to their putative target genes. This revealed that genes interacting with active enhancers had the highest expression levels, followed by genes interacting with primed enhancers, followed by genes interacting with poised enhancers.
June 2, 2025 at 11:32 PM
Using Promoter Capture Hi-C, we linked STARR-seq enhancers to their putative target genes. This revealed that genes interacting with active enhancers had the highest expression levels, followed by genes interacting with primed enhancers, followed by genes interacting with poised enhancers.
So, do current methods really capture the full active enhancer repertoire? We tested this systematically in human induced pluripotent stem cells using a blend of functional genomics, chromatin engineering and microscopy techniques, centered around STARR-seq (Stark lab @impvienna.bsky.social).
June 2, 2025 at 11:29 PM
So, do current methods really capture the full active enhancer repertoire? We tested this systematically in human induced pluripotent stem cells using a blend of functional genomics, chromatin engineering and microscopy techniques, centered around STARR-seq (Stark lab @impvienna.bsky.social).
An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq https://www.biorxiv.org/content/10.1101/2025.09.16.676677v1
September 17, 2025 at 12:34 PM
An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq https://www.biorxiv.org/content/10.1101/2025.09.16.676677v1
Suberin-rich roots can increase🌱stress resilience &help sequester carbon in the soil. We mapped the complete development of "plant amor" suberin-rich root phellem cells via single-nuclei sequencing and found a new regulator. #PlantScience @salkinstitute shorturl.at/ZFqLw
A single-nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation
Using small nuclear RNA sequencing (snRNA-seq), Miller et al. produced a gene expression census of the maturing Arabidopsis root and, by exploring the development of the suberizing phellem, identify that MYB67 controls phellem cell maturation. This census may serve as resource for engineering future plants with improved stress resilience and carbon capture capacity.
shorturl.at
January 9, 2025 at 4:12 PM
Suberin-rich roots can increase🌱stress resilience &help sequester carbon in the soil. We mapped the complete development of "plant amor" suberin-rich root phellem cells via single-nuclei sequencing and found a new regulator. #PlantScience @salkinstitute shorturl.at/ZFqLw
The main idea here is that by tagmenting tissue sections with polyA-tailed adapters, instead of the standard ATAC-seq adapters, we can use spatial transcriptomics slides from @10xgenomics.bsky.social to capture both ATAC and RNA data with spatial resolution. (2/5)
April 18, 2025 at 6:36 PM
The main idea here is that by tagmenting tissue sections with polyA-tailed adapters, instead of the standard ATAC-seq adapters, we can use spatial transcriptomics slides from @10xgenomics.bsky.social to capture both ATAC and RNA data with spatial resolution. (2/5)