FFPE and not yet FFPE.
August 23, 2026 at 5:01 PM
FFPE and not yet FFPE.
FFPE proteomics workflow on different instruments by Carr lab
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 24, 2024 at 9:39 PM
FFPE proteomics workflow on different instruments by Carr lab
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
(1/5)
🚨 New Research Alert! 🚨
Excited to share our latest work in @embojournal.bsky.social
"Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study" ✨
doi.org/10.1038/s443...
📌 Key Highlights:
🚨 New Research Alert! 🚨
Excited to share our latest work in @embojournal.bsky.social
"Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study" ✨
doi.org/10.1038/s443...
📌 Key Highlights:
Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study | The EMBO Journal
imageimageFormalin fixed paraffin embedded (FFPE) patient tumor specimens are readily accessible
and established gold standard for cancer diagnostics in pathology laboratories. To
start building a pan...
doi.org
December 13, 2024 at 11:38 AM
(1/5)
🚨 New Research Alert! 🚨
Excited to share our latest work in @embojournal.bsky.social
"Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study" ✨
doi.org/10.1038/s443...
📌 Key Highlights:
🚨 New Research Alert! 🚨
Excited to share our latest work in @embojournal.bsky.social
"Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study" ✨
doi.org/10.1038/s443...
📌 Key Highlights:
🚨 Now out in @aaas.org Science Advances 🚨: aDISCO: a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue by Anna Maria Reuss! 🧠🔬#lightsheet #Microscopy @mesospim.bsky.social @ptrrupprecht.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
August 12, 2026 at 6:43 PM
🚨 Now out in @aaas.org Science Advances 🚨: aDISCO: a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue by Anna Maria Reuss! 🧠🔬#lightsheet #Microscopy @mesospim.bsky.social @ptrrupprecht.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
The culmination of years of hard work by Anna Maria Reuss & Co: aDISCO - a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue! With lots of @mesospim.bsky.social #lightsheet #Microscopy @ptrrupprecht.bsky.social & many more!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
May 27, 2025 at 7:30 AM
The culmination of years of hard work by Anna Maria Reuss & Co: aDISCO - a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue! With lots of @mesospim.bsky.social #lightsheet #Microscopy @ptrrupprecht.bsky.social & many more!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A new preprint introduces aDISCO, a DISCO-based clearing approach that makes whole archival FFPE human tissues transparent and antibody-compatible, enabling true 3D light-sheet histology across brain & multiple organs at cellular resolution. Aguzzi & Helmchen teams.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 8, 2026 at 7:41 PM
A new preprint introduces aDISCO, a DISCO-based clearing approach that makes whole archival FFPE human tissues transparent and antibody-compatible, enabling true 3D light-sheet histology across brain & multiple organs at cellular resolution. Aguzzi & Helmchen teams.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Be on the lookout for a new paper from the lab:
"iCLAP: A high-plex immunostaining with high sensitivity for co-detection of low-abundance antigens".
In this paper, we introduce ICLAP to detect and spatially map low-abundance proteins, such as senescence markers, in FFPE tissue sections.
"iCLAP: A high-plex immunostaining with high sensitivity for co-detection of low-abundance antigens".
In this paper, we introduce ICLAP to detect and spatially map low-abundance proteins, such as senescence markers, in FFPE tissue sections.
April 5, 2025 at 3:20 PM
Be on the lookout for a new paper from the lab:
"iCLAP: A high-plex immunostaining with high sensitivity for co-detection of low-abundance antigens".
In this paper, we introduce ICLAP to detect and spatially map low-abundance proteins, such as senescence markers, in FFPE tissue sections.
"iCLAP: A high-plex immunostaining with high sensitivity for co-detection of low-abundance antigens".
In this paper, we introduce ICLAP to detect and spatially map low-abundance proteins, such as senescence markers, in FFPE tissue sections.
The Diagnosis of Mucormycosis by PCR: A Systematic Review & Meta-Analysis
Lottie Brown et al for @ishamycology.bsky.social Fungal PCR Initiative
Sn/Sp of Mucorales PCR on different samples:
Tissue 89%/87%
FFPE 71%/99%
BALF 97%/96%
Blood 81%/96%
papers.ssrn.com/sol3/papers.... #MedMycoSky #IDSky
Lottie Brown et al for @ishamycology.bsky.social Fungal PCR Initiative
Sn/Sp of Mucorales PCR on different samples:
Tissue 89%/87%
FFPE 71%/99%
BALF 97%/96%
Blood 81%/96%
papers.ssrn.com/sol3/papers.... #MedMycoSky #IDSky
January 17, 2025 at 3:41 PM
The Diagnosis of Mucormycosis by PCR: A Systematic Review & Meta-Analysis
Lottie Brown et al for @ishamycology.bsky.social Fungal PCR Initiative
Sn/Sp of Mucorales PCR on different samples:
Tissue 89%/87%
FFPE 71%/99%
BALF 97%/96%
Blood 81%/96%
papers.ssrn.com/sol3/papers.... #MedMycoSky #IDSky
Lottie Brown et al for @ishamycology.bsky.social Fungal PCR Initiative
Sn/Sp of Mucorales PCR on different samples:
Tissue 89%/87%
FFPE 71%/99%
BALF 97%/96%
Blood 81%/96%
papers.ssrn.com/sol3/papers.... #MedMycoSky #IDSky
Just picked up the beautiful offprint of our Patho-DBiT paper that was on the cover of Cell, highlighting its power to spatially explore molecular biology in human FFPE tissues 🤩🤩 . Congratulations to my phenomenal postdoc Zhiliang Bai and all amazing collaborators!!
January 28, 2025 at 9:26 PM
Just picked up the beautiful offprint of our Patho-DBiT paper that was on the cover of Cell, highlighting its power to spatially explore molecular biology in human FFPE tissues 🤩🤩 . Congratulations to my phenomenal postdoc Zhiliang Bai and all amazing collaborators!!
🌷Spring flowers? Fireworks?
Mouse cerebral cortex FFPE tissue was labeled with eight primary antibodies. Aluora Spatial Amplification Kits and DAPI were used for detection, followed by imaging on the EVOS S1000 Spatial Imaging System.
🧠🔬🧪 #Neuroscience #FluorescenceFriday
Mouse cerebral cortex FFPE tissue was labeled with eight primary antibodies. Aluora Spatial Amplification Kits and DAPI were used for detection, followed by imaging on the EVOS S1000 Spatial Imaging System.
🧠🔬🧪 #Neuroscience #FluorescenceFriday
March 21, 2025 at 5:27 AM
🌷Spring flowers? Fireworks?
Mouse cerebral cortex FFPE tissue was labeled with eight primary antibodies. Aluora Spatial Amplification Kits and DAPI were used for detection, followed by imaging on the EVOS S1000 Spatial Imaging System.
🧠🔬🧪 #Neuroscience #FluorescenceFriday
Mouse cerebral cortex FFPE tissue was labeled with eight primary antibodies. Aluora Spatial Amplification Kits and DAPI were used for detection, followed by imaging on the EVOS S1000 Spatial Imaging System.
🧠🔬🧪 #Neuroscience #FluorescenceFriday
Once upon a time, FFPE was considered a death knell for studying molecular biology in archived cancer samples.
So many wonderful advances in this area now make FFPE a rich source for study of RNA, DNA and protein.
Check out this new gem. 💎
#proteomics
#genomics
www.biorxiv.org/content/10.1...
So many wonderful advances in this area now make FFPE a rich source for study of RNA, DNA and protein.
Check out this new gem. 💎
#proteomics
#genomics
www.biorxiv.org/content/10.1...
High-throughput proteomic and phosphoproteomic analysis of formalin-fixed paraffin-embedded tissue
Formalin-fixed paraffin-embedded FFPE patient tissues are a valuable resource for proteomic studies with the potential to associate the derived molecular insights with clinical outcomes. Here we prese...
www.biorxiv.org
November 20, 2024 at 8:20 PM
Once upon a time, FFPE was considered a death knell for studying molecular biology in archived cancer samples.
So many wonderful advances in this area now make FFPE a rich source for study of RNA, DNA and protein.
Check out this new gem. 💎
#proteomics
#genomics
www.biorxiv.org/content/10.1...
So many wonderful advances in this area now make FFPE a rich source for study of RNA, DNA and protein.
Check out this new gem. 💎
#proteomics
#genomics
www.biorxiv.org/content/10.1...
🧧🧧🧧🧧 So another exciting finding for the weekend before I go on vacation.
*FFPE Ligation Sequencing for ALL!*
For a long while it was thought that ligation (i.e. native DNA) sequencing on @nanoporetech.com was difficult, if not impossible.
*FFPE Ligation Sequencing for ALL!*
For a long while it was thought that ligation (i.e. native DNA) sequencing on @nanoporetech.com was difficult, if not impossible.
April 13, 2025 at 8:30 AM
🧧🧧🧧🧧 So another exciting finding for the weekend before I go on vacation.
*FFPE Ligation Sequencing for ALL!*
For a long while it was thought that ligation (i.e. native DNA) sequencing on @nanoporetech.com was difficult, if not impossible.
*FFPE Ligation Sequencing for ALL!*
For a long while it was thought that ligation (i.e. native DNA) sequencing on @nanoporetech.com was difficult, if not impossible.
Comparing Imaging-based #SpatialTranscriptimics methods
CosMx vs MERFISH vs Xenium
1k vs 500 vs 339 plex
FFPE👤Lung/Mesothelium Tumor Microarray
CosMX▶️highest transcript counts/cell
Xenium▶️lowest FDR & highest cell segmentation precision
bioRxiv 2024
www.biorxiv.org/content/10.1...
CosMx vs MERFISH vs Xenium
1k vs 500 vs 339 plex
FFPE👤Lung/Mesothelium Tumor Microarray
CosMX▶️highest transcript counts/cell
Xenium▶️lowest FDR & highest cell segmentation precision
bioRxiv 2024
www.biorxiv.org/content/10.1...
December 19, 2024 at 12:21 PM
Comparing Imaging-based #SpatialTranscriptimics methods
CosMx vs MERFISH vs Xenium
1k vs 500 vs 339 plex
FFPE👤Lung/Mesothelium Tumor Microarray
CosMX▶️highest transcript counts/cell
Xenium▶️lowest FDR & highest cell segmentation precision
bioRxiv 2024
www.biorxiv.org/content/10.1...
CosMx vs MERFISH vs Xenium
1k vs 500 vs 339 plex
FFPE👤Lung/Mesothelium Tumor Microarray
CosMX▶️highest transcript counts/cell
Xenium▶️lowest FDR & highest cell segmentation precision
bioRxiv 2024
www.biorxiv.org/content/10.1...
Comparing single-cell #SpatialTranscriptomics methods on FFPE human tumor #TissueMicroArray
CosMx 1k vs MERFISH 500 vs Xenium-UM/-MM 339
93 common genes
lung adenocarcinoma
pleural mesothelioma
Corr. Bulk RNAseq, GeoMx
#NatureComms 2025
www.nature.com/articles/s41...
CosMx 1k vs MERFISH 500 vs Xenium-UM/-MM 339
93 common genes
lung adenocarcinoma
pleural mesothelioma
Corr. Bulk RNAseq, GeoMx
#NatureComms 2025
www.nature.com/articles/s41...
September 28, 2025 at 12:22 PM
Comparing single-cell #SpatialTranscriptomics methods on FFPE human tumor #TissueMicroArray
CosMx 1k vs MERFISH 500 vs Xenium-UM/-MM 339
93 common genes
lung adenocarcinoma
pleural mesothelioma
Corr. Bulk RNAseq, GeoMx
#NatureComms 2025
www.nature.com/articles/s41...
CosMx 1k vs MERFISH 500 vs Xenium-UM/-MM 339
93 common genes
lung adenocarcinoma
pleural mesothelioma
Corr. Bulk RNAseq, GeoMx
#NatureComms 2025
www.nature.com/articles/s41...
Talking to non biologist- computational scientists, who asked what "FFPE" meant.
"FFPE: Latin for 'degraded nucleic acid.' 🧬 Because who needs high-quality DNA when you’ve got thousands of blocks packed with low-quality nucleic acids? " #GenomicsHumor #ScienceLife
"FFPE: Latin for 'degraded nucleic acid.' 🧬 Because who needs high-quality DNA when you’ve got thousands of blocks packed with low-quality nucleic acids? " #GenomicsHumor #ScienceLife
December 2, 2024 at 7:59 PM
Talking to non biologist- computational scientists, who asked what "FFPE" meant.
"FFPE: Latin for 'degraded nucleic acid.' 🧬 Because who needs high-quality DNA when you’ve got thousands of blocks packed with low-quality nucleic acids? " #GenomicsHumor #ScienceLife
"FFPE: Latin for 'degraded nucleic acid.' 🧬 Because who needs high-quality DNA when you’ve got thousands of blocks packed with low-quality nucleic acids? " #GenomicsHumor #ScienceLife
Despite the obvious superiority of fresh-frozen material for genomics, many samples are still stored in FFPE and remain challenging to characterize with Whole-genome sequencing. But here comes our solution:
An explainable boosting machine model for identifying artifacts caused by formalin-fixed paraffin embedding https://www.biorxiv.org/content/10.64898/2026.03.10.710815v1
March 14, 2026 at 6:44 PM
Despite the obvious superiority of fresh-frozen material for genomics, many samples are still stored in FFPE and remain challenging to characterize with Whole-genome sequencing. But here comes our solution:
Another chapter of my PhD thesis has been published! We observed a strong overlap and correlation between #FFPE (formalin-fixed paraffin-embedded) and FF (fresh-frozen) tissues in #proteomics and #phosphoproteomics.
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
February 18, 2025 at 9:11 AM
Another chapter of my PhD thesis has been published! We observed a strong overlap and correlation between #FFPE (formalin-fixed paraffin-embedded) and FF (fresh-frozen) tissues in #proteomics and #phosphoproteomics.
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Dropping another one for #FluorescenceFriday #Valentine's.
FFPE Human Duodenum Tissue, EVOS M7000 20X. Primary antibody staining for P53, SMA, PCNA, EpCam, HLA-DR plus DAPI.
FFPE Human Duodenum Tissue, EVOS M7000 20X. Primary antibody staining for P53, SMA, PCNA, EpCam, HLA-DR plus DAPI.
February 14, 2025 at 11:41 PM
Dropping another one for #FluorescenceFriday #Valentine's.
FFPE Human Duodenum Tissue, EVOS M7000 20X. Primary antibody staining for P53, SMA, PCNA, EpCam, HLA-DR plus DAPI.
FFPE Human Duodenum Tissue, EVOS M7000 20X. Primary antibody staining for P53, SMA, PCNA, EpCam, HLA-DR plus DAPI.
While C3 by pronase IF on FFPE is less sensitive/reliable, it can still be helpful when positive. Left frozen C3, right FFPE C3 from a case of recurrent C3GN in a txp. Did IF par to rule out masked deposits just in case (there were non). So the stain can work. #renalpath #pathsky #nephsky
January 24, 2025 at 11:37 PM
While C3 by pronase IF on FFPE is less sensitive/reliable, it can still be helpful when positive. Left frozen C3, right FFPE C3 from a case of recurrent C3GN in a txp. Did IF par to rule out masked deposits just in case (there were non). So the stain can work. #renalpath #pathsky #nephsky
Spatial FFPE ATAC-seq has arrived!
Profile open chromatin in preserved FFPE tissue with 10 µm resolution — and see our first FFPE kidney dataset live on the
AtlasXomics data portal : lnkd.in/e-8sTMnY
#SpatialBiology #Epigenetics #CancerResearch
Profile open chromatin in preserved FFPE tissue with 10 µm resolution — and see our first FFPE kidney dataset live on the
AtlasXomics data portal : lnkd.in/e-8sTMnY
#SpatialBiology #Epigenetics #CancerResearch
November 13, 2025 at 5:13 PM
Spatial FFPE ATAC-seq has arrived!
Profile open chromatin in preserved FFPE tissue with 10 µm resolution — and see our first FFPE kidney dataset live on the
AtlasXomics data portal : lnkd.in/e-8sTMnY
#SpatialBiology #Epigenetics #CancerResearch
Profile open chromatin in preserved FFPE tissue with 10 µm resolution — and see our first FFPE kidney dataset live on the
AtlasXomics data portal : lnkd.in/e-8sTMnY
#SpatialBiology #Epigenetics #CancerResearch
@science.org RNA polymerase II at histone genes predicts outcome in human cancer 🧬💊 @fredhutch.bsky.social @hhmi.bsky.social www.science.org/doi/10.1126/...
February 16, 2025 at 11:25 PM
@science.org RNA polymerase II at histone genes predicts outcome in human cancer 🧬💊 @fredhutch.bsky.social @hhmi.bsky.social www.science.org/doi/10.1126/...
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...
#SpatialRNAEncyclopedia
Patho-DBiT
#SpatialTranscriptomics FFPE
Spatial Co-mapping of RNA Expression Splicing Editing SNV AND ncRNAs (miRNA lncRNA rRNA snRNA)👹
in situ polyA tailing
10 μm/px➡️ >2000 genes Lymphoma
@rongfan8.bsky.social @cellcellpress.bsky.social 2025
www.cell.com/cell/fulltex...
Patho-DBiT
#SpatialTranscriptomics FFPE
Spatial Co-mapping of RNA Expression Splicing Editing SNV AND ncRNAs (miRNA lncRNA rRNA snRNA)👹
in situ polyA tailing
10 μm/px➡️ >2000 genes Lymphoma
@rongfan8.bsky.social @cellcellpress.bsky.social 2025
www.cell.com/cell/fulltex...
February 24, 2025 at 12:49 PM
#SpatialRNAEncyclopedia
Patho-DBiT
#SpatialTranscriptomics FFPE
Spatial Co-mapping of RNA Expression Splicing Editing SNV AND ncRNAs (miRNA lncRNA rRNA snRNA)👹
in situ polyA tailing
10 μm/px➡️ >2000 genes Lymphoma
@rongfan8.bsky.social @cellcellpress.bsky.social 2025
www.cell.com/cell/fulltex...
Patho-DBiT
#SpatialTranscriptomics FFPE
Spatial Co-mapping of RNA Expression Splicing Editing SNV AND ncRNAs (miRNA lncRNA rRNA snRNA)👹
in situ polyA tailing
10 μm/px➡️ >2000 genes Lymphoma
@rongfan8.bsky.social @cellcellpress.bsky.social 2025
www.cell.com/cell/fulltex...
Formalin-fixed, paraffin-embedded (FFPE) tissues in oncology diagnostics: is there a better way? 🧬 🧪
FFPE Sucks.
Formalin-fixed, paraffin-embedded (FFPE) tissues in oncology diagnostics: is there a better way?
buff.ly
February 13, 2025 at 4:05 PM
Formalin-fixed, paraffin-embedded (FFPE) tissues in oncology diagnostics: is there a better way? 🧬 🧪