FYI: New online! Spatial multi-omics of nuclear architecture with two-layer seqFISH+
Spatial multi-omics of nuclear architecture with two-layer seqFISH+
Nature Reviews Genetics, Published online: 25 June 2025; doi:10.1038/s41576-025-00868-5In this Tools of the Trade article, Yodai Takei presents two-layer seqFISH+, an imaging method that uses a novel barcoding strategy to simultaneously profile chromatin organization, the transcriptome and subnuclear structures at single-cell resolution.
www.nature.com
July 16, 2025 at 12:32 PM
FYI: New online! Spatial multi-omics of nuclear architecture with two-layer seqFISH+
Nature research paper: Spatial multi-omics reveals cell-type-specific nuclear compartments
https://go.nature.com/4jngJJB
https://go.nature.com/4jngJJB
Spatial multi-omics reveals cell-type-specific nuclear compartments - Nature
A genomic barcoding scheme called two-layer DNA seqFISH+ enables the simultaneous mapping of more than 100,000 loci and has been used to identify cell-type-specific subnuclear compartments in the mouse brain.
go.nature.com
April 10, 2025 at 9:47 AM
Nature research paper: Spatial multi-omics reveals cell-type-specific nuclear compartments
https://go.nature.com/4jngJJB
https://go.nature.com/4jngJJB
Amazing 🚀 study w/ DNA seqFISH+, enabling mapping of 100,049 genomic loci, together with the nascent transcriptome for 17,856 genes, yielding unpredented insights into subnuclear structures in single cells www.nature.com/articles/s41...
Spatial multi-omics reveals cell-type-specific nuclear compartments - Nature
A genomic barcoding scheme called two-layer DNA seqFISH+ enables the simultaneous mapping of more than 100,000 loci and has been used to identify cell-type-specific subnuclear compartments in the mous...
www.nature.com
April 13, 2025 at 2:15 PM
Amazing 🚀 study w/ DNA seqFISH+, enabling mapping of 100,049 genomic loci, together with the nascent transcriptome for 17,856 genes, yielding unpredented insights into subnuclear structures in single cells www.nature.com/articles/s41...
Spatial multi-omics reveals cell-type-specific nuclear compartments www.nature.com/articles/s41...
Spatial multi-omics reveals cell-type-specific nuclear compartments - Nature
A genomic barcoding scheme called two-layer DNA seqFISH+ enables the simultaneous mapping of more than 100,000 loci and has been used to identify cell-type-specific subnuclear compartments in the mous...
www.nature.com
June 27, 2025 at 9:33 AM
Spatial multi-omics reveals cell-type-specific nuclear compartments www.nature.com/articles/s41...
Spatial multi-omics reveals cell-type-specific nuclear compartments | Nature
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Spatial multi-omics reveals cell-type-specific nuclear compartments - Nature
A genomic barcoding scheme called two-layer DNA seqFISH+ enables the simultaneous mapping of more than 100,000 loci and has been used to identify cell-type-specific subnuclear compartments in the mous...
www.nature.com
June 27, 2025 at 5:54 AM
Spatial multi-omics reveals cell-type-specific nuclear compartments | Nature
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ICYMI: New online! Spatial multi-omics of nuclear architecture with two-layer seqFISH+
Spatial multi-omics of nuclear architecture with two-layer seqFISH+
Nature Reviews Genetics, Published online: 25 June 2025; doi:10.1038/s41576-025-00868-5In this Tools of the Trade article, Yodai Takei presents two-layer seqFISH+, an imaging method that uses a novel barcoding strategy to simultaneously profile chromatin organization, the transcriptome and subnuclear structures at single-cell resolution.
www.nature.com
July 2, 2025 at 12:30 PM
ICYMI: New online! Spatial multi-omics of nuclear architecture with two-layer seqFISH+
In #SpatialBiology news, a preprint on CKD using seqFISH www.biorxiv.org/content/10.1...
November 27, 2023 at 9:00 AM
In #SpatialBiology news, a preprint on CKD using seqFISH www.biorxiv.org/content/10.1...
Check out this nice "Tools of the Trade" piece in Nature Reviews Genetics written by Ankit Agrawal on our NiCo algorithm for the analysis of single-cell spatial transcriptomics data from platforms like Xenium, MERSCOPE, seqFISH etc.
Feel free to reach out for advice.
www.nature.com/articles/s41...
Feel free to reach out for advice.
www.nature.com/articles/s41...
Decoding cell–cell communication using spatial transcriptomics - Nature Reviews Genetics
In this Tools of the Trade article, Ankit Agrawal introduces the computational framework NiCo (Niche Covariation), which integrates spatial transcriptomics with single-cell RNA-sequencing data to stud...
www.nature.com
February 21, 2025 at 3:35 PM
Check out this nice "Tools of the Trade" piece in Nature Reviews Genetics written by Ankit Agrawal on our NiCo algorithm for the analysis of single-cell spatial transcriptomics data from platforms like Xenium, MERSCOPE, seqFISH etc.
Feel free to reach out for advice.
www.nature.com/articles/s41...
Feel free to reach out for advice.
www.nature.com/articles/s41...
New study using seqFISH+ reveals 2,653 genes in 867,062 mouse testis cells, mapping the seminiferous cycle and showing Sertoli cells' unique cyclic transcription aligned with spermatogenesis! PMID:42143021, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S009286742600471X #Medsky #Pharmsky 🧪
https://www.cell.com/cell/fulltext/S009286742600471X
No description available
www.cell.com
July 12, 2026 at 8:00 PM
New study using seqFISH+ reveals 2,653 genes in 867,062 mouse testis cells, mapping the seminiferous cycle and showing Sertoli cells' unique cyclic transcription aligned with spermatogenesis! PMID:42143021, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S009286742600471X #Medsky #Pharmsky 🧪
New online! Spatial multi-omics of nuclear architecture with two-layer seqFISH+
Spatial multi-omics of nuclear architecture with two-layer seqFISH+
Nature Reviews Genetics, Published online: 25 June 2025; doi:10.1038/s41576-025-00868-5In this Tools of the Trade article, Yodai Takei presents two-layer seqFISH+, an imaging method that uses a novel barcoding strategy to simultaneously profile chromatin organization, the transcriptome and subnuclear structures at single-cell resolution.
www.nature.com
June 25, 2025 at 12:29 PM
New online! Spatial multi-omics of nuclear architecture with two-layer seqFISH+
Daniel introduces par-seqFISH that he developed as post doc with Dianne Newman to follow phenotypic heterogeneity of over hundred genes in Pseudomonas aeruginosa biofilms
See their @science.org publication:
www.science.org/doi/full/10....
#MultiBac2025
See their @science.org publication:
www.science.org/doi/full/10....
#MultiBac2025
Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution
Spatially resolved, parallel transcriptome imaging reveals functional heterogeneity in bacterial cultures and biofilms.
www.science.org
January 8, 2025 at 8:10 AM
Daniel introduces par-seqFISH that he developed as post doc with Dianne Newman to follow phenotypic heterogeneity of over hundred genes in Pseudomonas aeruginosa biofilms
See their @science.org publication:
www.science.org/doi/full/10....
#MultiBac2025
See their @science.org publication:
www.science.org/doi/full/10....
#MultiBac2025
New data: Spatial transcriptomics (using seqFISH) reveals a fibroblast-immune microenvironment remodeling pathway in CFA-induced TMJ arthritis in mice. PI: Jian-Fu Chen (University of Southern California)
doi.org/10.25550/8Q-...
doi.org/10.25550/8Q-...
March 5, 2026 at 5:56 PM
New data: Spatial transcriptomics (using seqFISH) reveals a fibroblast-immune microenvironment remodeling pathway in CFA-induced TMJ arthritis in mice. PI: Jian-Fu Chen (University of Southern California)
doi.org/10.25550/8Q-...
doi.org/10.25550/8Q-...
Amazing insights into single cell transcriptional heterogeneity of Pseudomonas QS system using Par-seqFISH
talk by Danielle Gabi (Daniel Dar group) on Lange On Structured Heterogeneity Within a Synchronizing Quorum Sensing Network
#EMBOBacNet
talk by Danielle Gabi (Daniel Dar group) on Lange On Structured Heterogeneity Within a Synchronizing Quorum Sensing Network
#EMBOBacNet
September 14, 2026 at 3:19 PM
Amazing insights into single cell transcriptional heterogeneity of Pseudomonas QS system using Par-seqFISH
talk by Danielle Gabi (Daniel Dar group) on Lange On Structured Heterogeneity Within a Synchronizing Quorum Sensing Network
#EMBOBacNet
talk by Danielle Gabi (Daniel Dar group) on Lange On Structured Heterogeneity Within a Synchronizing Quorum Sensing Network
#EMBOBacNet
This is game changer!!
Spatial multi-omics reveals cell-type-specific nuclear compartments
Two-layer DNA seqFISH+
Simultaneous mapping of 100,049 genomic loci
+ nascent transcriptome for 17,856 genes in single cells
www.nature.com/articles/s41...
Spatial multi-omics reveals cell-type-specific nuclear compartments
Two-layer DNA seqFISH+
Simultaneous mapping of 100,049 genomic loci
+ nascent transcriptome for 17,856 genes in single cells
www.nature.com/articles/s41...
April 10, 2025 at 10:03 PM
This is game changer!!
Spatial multi-omics reveals cell-type-specific nuclear compartments
Two-layer DNA seqFISH+
Simultaneous mapping of 100,049 genomic loci
+ nascent transcriptome for 17,856 genes in single cells
www.nature.com/articles/s41...
Spatial multi-omics reveals cell-type-specific nuclear compartments
Two-layer DNA seqFISH+
Simultaneous mapping of 100,049 genomic loci
+ nascent transcriptome for 17,856 genes in single cells
www.nature.com/articles/s41...
Using image-based spatial transcriptomics (seqFISH, CosMX, Xenium, etc.) and cell shape-based mechanical force inference, spatial mechano-transcriptomics allows simultaneous spatial profiling of gene expression and mechanical forces at single cell resolution.
March 17, 2025 at 12:53 PM
Using image-based spatial transcriptomics (seqFISH, CosMX, Xenium, etc.) and cell shape-based mechanical force inference, spatial mechano-transcriptomics allows simultaneous spatial profiling of gene expression and mechanical forces at single cell resolution.
Nerves don't just wire up muscle - they help build it. New in FaceBase: single-cell, bulk RNA-seq, and SeqFISH showing trigeminal nerve-derived GDF11 shaping soft palate muscle architecture. @ccmb.usc.edu #craniofacial #devbio #scRNAseq #spatialtranscriptomics
www.facebase.org/2026/08/25/r...
www.facebase.org/2026/08/25/r...
New release: Sensory nerve-derived signaling coordinates oropharyngeal structural organization that supports suckling and vocalization in neonatal mice
A new dataset from the Chai lab at the University of Southern California is now available in FaceBase, combining single-cell RNA sequencing, bulk RNA sequencing, and SeqFISH spatial transcriptomics to...
www.facebase.org
August 27, 2026 at 8:19 PM
Nerves don't just wire up muscle - they help build it. New in FaceBase: single-cell, bulk RNA-seq, and SeqFISH showing trigeminal nerve-derived GDF11 shaping soft palate muscle architecture. @ccmb.usc.edu #craniofacial #devbio #scRNAseq #spatialtranscriptomics
www.facebase.org/2026/08/25/r...
www.facebase.org/2026/08/25/r...
We demonstrate TOAST on tasks of intra-, intersample, and temporal alignment in:
🧠 Human cortical layers (Visium)
🧫 Axolotl regeneration (Stereo-seq)
🐭 Locallization in mouse embryo development (seqFISH)
🎯 Various cancer types (IMC)
... with state-of-the-art efficiency and performance.
🧠 Human cortical layers (Visium)
🧫 Axolotl regeneration (Stereo-seq)
🐭 Locallization in mouse embryo development (seqFISH)
🎯 Various cancer types (IMC)
... with state-of-the-art efficiency and performance.
April 22, 2025 at 9:37 AM
We demonstrate TOAST on tasks of intra-, intersample, and temporal alignment in:
🧠 Human cortical layers (Visium)
🧫 Axolotl regeneration (Stereo-seq)
🐭 Locallization in mouse embryo development (seqFISH)
🎯 Various cancer types (IMC)
... with state-of-the-art efficiency and performance.
🧠 Human cortical layers (Visium)
🧫 Axolotl regeneration (Stereo-seq)
🐭 Locallization in mouse embryo development (seqFISH)
🎯 Various cancer types (IMC)
... with state-of-the-art efficiency and performance.
Spatial multi-omics reveals cell-type-specific nuclear compartments | Nature www.nature.com/articles/s41...
Spatial multi-omics reveals cell-type-specific nuclear compartments - Nature
A genomic barcoding scheme called two-layer DNA seqFISH+ enables the simultaneous mapping of more than 100,000 loci and has been used to identify cell-type-specific subnuclear compartments in the mous...
www.nature.com
April 11, 2025 at 12:16 AM
Spatial multi-omics reveals cell-type-specific nuclear compartments | Nature www.nature.com/articles/s41...
Illuminating article with Dar as final author:
‘Single-cell phenotypic heterogeneity shapes quorum signaling dynamics in Pseudomonas aeruginosa’
tinyurl.com/mw6z4wes
#WIS
#PlantandEnvironmentalScience
#QuorumSensing
Fig.1 Par-seqFISH imaging of the P. aeruginosa QS response
Fig.1a
‘Single-cell phenotypic heterogeneity shapes quorum signaling dynamics in Pseudomonas aeruginosa’
tinyurl.com/mw6z4wes
#WIS
#PlantandEnvironmentalScience
#QuorumSensing
Fig.1 Par-seqFISH imaging of the P. aeruginosa QS response
Fig.1a
April 16, 2026 at 11:10 AM
Illuminating article with Dar as final author:
‘Single-cell phenotypic heterogeneity shapes quorum signaling dynamics in Pseudomonas aeruginosa’
tinyurl.com/mw6z4wes
#WIS
#PlantandEnvironmentalScience
#QuorumSensing
Fig.1 Par-seqFISH imaging of the P. aeruginosa QS response
Fig.1a
‘Single-cell phenotypic heterogeneity shapes quorum signaling dynamics in Pseudomonas aeruginosa’
tinyurl.com/mw6z4wes
#WIS
#PlantandEnvironmentalScience
#QuorumSensing
Fig.1 Par-seqFISH imaging of the P. aeruginosa QS response
Fig.1a
excited to be on Bluesky now! The oligo-designer-toolsuite developed at @helmholtzai.bsky.social @www.helmholtz-munich.de is for you when you:
🧬 need to design oligos
🧪 use technologies such as #merfish #seqfish #scrinshot
🖥️ design a pipeline for a new technology
github.com/HelmholtzAI-...
🧬 need to design oligos
🧪 use technologies such as #merfish #seqfish #scrinshot
🖥️ design a pipeline for a new technology
github.com/HelmholtzAI-...
GitHub - HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite: Develop custom oligo design pipelines.
Develop custom oligo design pipelines. Contribute to HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite development by creating an account on GitHub.
github.com
July 10, 2025 at 1:16 PM
excited to be on Bluesky now! The oligo-designer-toolsuite developed at @helmholtzai.bsky.social @www.helmholtz-munich.de is for you when you:
🧬 need to design oligos
🧪 use technologies such as #merfish #seqfish #scrinshot
🖥️ design a pipeline for a new technology
github.com/HelmholtzAI-...
🧬 need to design oligos
🧪 use technologies such as #merfish #seqfish #scrinshot
🖥️ design a pipeline for a new technology
github.com/HelmholtzAI-...
こちらの論文、
www.biorxiv.org/content/10.1...
リバイスなどで時間かかりましたが、そのおかげでかなり洗練された形になって、アクセプト頂きました。
seqFISH データのサンプル間揺らぎに着目すると、割と素朴な解析で、染色体毎に異なる動態の特徴、染色体間の核内位置関係、染色体ー核内構造体間の配置関係、細胞周期との関係、などなど核内の事情が色々わかりそう！という感じです。
1st author の本来ウェット系のラボの学生さんが、ドライ-数理的を本当によく解析頑張りました。おめでとう！！
www.biorxiv.org/content/10.1...
リバイスなどで時間かかりましたが、そのおかげでかなり洗練された形になって、アクセプト頂きました。
seqFISH データのサンプル間揺らぎに着目すると、割と素朴な解析で、染色体毎に異なる動態の特徴、染色体間の核内位置関係、染色体ー核内構造体間の配置関係、細胞周期との関係、などなど核内の事情が色々わかりそう！という感じです。
1st author の本来ウェット系のラボの学生さんが、ドライ-数理的を本当によく解析頑張りました。おめでとう！！
Identification of anisotropy in chromosome dynamics by principal component analysis using integrated spatial genomics
Eukaryotic interphase chromosomes maintain a three-dimensional structure within the nucleus and undergo fluctuations. It has been reported that such dynamics are involved in transcription, replication...
www.biorxiv.org
May 17, 2025 at 4:15 AM
こちらの論文、
www.biorxiv.org/content/10.1...
リバイスなどで時間かかりましたが、そのおかげでかなり洗練された形になって、アクセプト頂きました。
seqFISH データのサンプル間揺らぎに着目すると、割と素朴な解析で、染色体毎に異なる動態の特徴、染色体間の核内位置関係、染色体ー核内構造体間の配置関係、細胞周期との関係、などなど核内の事情が色々わかりそう！という感じです。
1st author の本来ウェット系のラボの学生さんが、ドライ-数理的を本当によく解析頑張りました。おめでとう！！
www.biorxiv.org/content/10.1...
リバイスなどで時間かかりましたが、そのおかげでかなり洗練された形になって、アクセプト頂きました。
seqFISH データのサンプル間揺らぎに着目すると、割と素朴な解析で、染色体毎に異なる動態の特徴、染色体間の核内位置関係、染色体ー核内構造体間の配置関係、細胞周期との関係、などなど核内の事情が色々わかりそう！という感じです。
1st author の本来ウェット系のラボの学生さんが、ドライ-数理的を本当によく解析頑張りました。おめでとう！！
We're excited to share our latest publication from Chai lab in
@natcomms.nature.com titled "High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development." rdcu.be/elKQ0 #CCMBUSC #CraniofacialResearch #seqFISH
@natcomms.nature.com titled "High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development." rdcu.be/elKQ0 #CCMBUSC #CraniofacialResearch #seqFISH
High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development
Nature Communications - Neural crest cells differentiate into distinct fates during craniofacial morphogenesis, though how these are acquired remains unclear. Here they show that mesenchymal...
rdcu.be
May 13, 2025 at 12:46 AM
We're excited to share our latest publication from Chai lab in
@natcomms.nature.com titled "High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development." rdcu.be/elKQ0 #CCMBUSC #CraniofacialResearch #seqFISH
@natcomms.nature.com titled "High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development." rdcu.be/elKQ0 #CCMBUSC #CraniofacialResearch #seqFISH
Revolutionizing understanding of spermatogenesis! Using seqFISH+ spatial transcriptomics, 2,653 genes in 867,062 testis cells reveal tubule-level transcriptional cycles in Sertoli cells. A breakthrough in mapping… PMID:42143021, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S009286742600471X
https://www.cell.com/cell/fulltext/S009286742600471X
No description available
www.cell.com
July 30, 2026 at 12:00 AM
Revolutionizing understanding of spermatogenesis! Using seqFISH+ spatial transcriptomics, 2,653 genes in 867,062 testis cells reveal tubule-level transcriptional cycles in Sertoli cells. A breakthrough in mapping… PMID:42143021, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S009286742600471X
Revolutionizing spermatogenesis study! Using seqFISH+, 2,653 genes in 867,062 mouse testis cells uncovered a cyclical tubule transcription pattern, highlighting Sertoli cells' unique sync with germ-cell… PMID:42143021, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S009286742600471X #Medsky 🧪
https://www.cell.com/cell/fulltext/S009286742600471X
No description available
www.cell.com
July 16, 2026 at 3:00 PM
Revolutionizing spermatogenesis study! Using seqFISH+, 2,653 genes in 867,062 mouse testis cells uncovered a cyclical tubule transcription pattern, highlighting Sertoli cells' unique sync with germ-cell… PMID:42143021, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S009286742600471X #Medsky 🧪