Simple, Fast and Highly Efficient One-or Two-step Proteomic Preparation Enables Deep Profiling of Microgram-level FF and FFPE Tissues www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
October 10, 2025 at 8:20 PM
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🧪🧬 Biobanked FFPE tissues are a massive resource in biomedical research, but are incompatible with most chromatin profiling assays.
Can newer strategies - like CUT&Tag - help solve this problem?
See @emadden.bsky.social talk about our progress at Keystone Precision Oncology, Jan 15, to learn more!
Can newer strategies - like CUT&Tag - help solve this problem?
See @emadden.bsky.social talk about our progress at Keystone Precision Oncology, Jan 15, to learn more!
January 10, 2025 at 5:32 PM
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a long time to prepare and thus is not feasible during surgery. To help pathologists observe IHC images with high quality in surgery, this paper proposes a Cross-REsolution compensATed and multi-frequency Enhanced FS-to-FFPE [3/8 of https://arxiv.org/abs/2503.00697v1]
March 4, 2025 at 6:28 AM
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🔬 Key Findings:
-Using an innovative FFPE-RNAPII mapping method, global RNA polymerase II (RNAPII) elevations were observed in human tumors and mouse gliomas.
-Regional RNAPII increases corresponded to HER2 amplifications and chromosome losses in cancers.
-Using an innovative FFPE-RNAPII mapping method, global RNA polymerase II (RNAPII) elevations were observed in human tumors and mouse gliomas.
-Regional RNAPII increases corresponded to HER2 amplifications and chromosome losses in cancers.
February 14, 2025 at 1:30 AM
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I’ve led a “proteomics CRO” since 2017 and the service most needed and accepted in pharma is the targeted MS assay with stable isotope labeled standards. Measurement in cells or tissue, including FFPE is what connects.
November 19, 2024 at 7:54 PM
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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
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Had a nice trip to the Center for Comparative Genomics @calacademy.bsky.social recently for a workshop—got to learn library prep for degraded/historic/museum samples using New England Biolabs FFPE kit. Easy protocol and it gave great results in my case from a 130 y.o. herbarium sample (flax)!
December 10, 2024 at 11:47 PM
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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
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🧧🧧🧧🧧 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
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Clearing method adapted to FFPE tissues for 3D imaging of nerve fibers, B cells, and tertiary lymphoid structures https://www.biorxiv.org/content/10.1101/2024.05.05.592575v1
Clearing method adapted to FFPE tissues for 3D imaging of nerve fibers, B cells, and tertiary lymphoid structures https://www.biorxiv.org/content/10.1101/2024.05.05.592575v1
Biomedical samples are commonly used for histological examination after their inclusion in paraffin
www.biorxiv.org
May 6, 2024 at 5:23 AM
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problems such as image contamination and poor nuclear detail, which may disturb the pathologist's diagnosis. In contrast, formalin-fixed and paraffin-embedded (FFPE) image has a higher staining quality, but it requires quite [2/8 of https://arxiv.org/abs/2503.00697v1]
March 4, 2025 at 6:28 AM
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Hoy les he propuesto a mis alumnos la práctica de desparafinación de tejido FFPE y ha ido todo bien salvo porque he puesto mi primer parte en el centro
November 13, 2024 at 11:21 PM
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3/ What is your diagnosis based on the provided H&E stained frozen and FFPE section images?
April 21, 2025 at 1:03 PM
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Reminder: Our free webinar is tomorrow, 11 June at 2.00 p.m. BST.
Join our experts for a live Q&A on DNA and RNA extraction from complex samples like FFPE and liquid biopsies.
Register here: https://bit.ly/3HDmTHU
#MolecularGenetics #HighThroughput
Join our experts for a live Q&A on DNA and RNA extraction from complex samples like FFPE and liquid biopsies.
Register here: https://bit.ly/3HDmTHU
#MolecularGenetics #HighThroughput
June 10, 2025 at 8:17 AM
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FFPE Tissue Samples Market Size, Growth, Trends, Report 2035 www.marketresearchfuture.com/reports/ffpe...
FFPE Tissue Samples Market Size, Growth, Trends, Report 2035
FFPE Tissue Samples Market is projected to register a CAGR of 5.8% to reach USD 9.14 Billion by the end of 2035, FFPE Tissue Samples Market Type, Application, Format, Preservation Method, Region | FFP...
www.marketresearchfuture.com
October 10, 2025 at 7:27 AM
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News in Proteomics Research blog post | 1,220 FFPE Tissues analyzed at >4,000 protein depth/sample! proteomicsnews.blogs...
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#proteomics #prot-other
July 10, 2024 at 12:20 PM
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Reliable RNA-seq analysis from FFPE specimens as a means to accelerate cancer-related health disparities research https://www.biorxiv.org/content/10.1101/2024.10.10.617597v1
Reliable RNA-seq analysis from FFPE specimens as a means to accelerate cancer-related health disparities research https://www.biorxiv.org/content/10.1101/2024.10.10.617597v1
Whole transcriptome sequencing (WTS/ RNA-Seq) is a ubiquitous tool for investigating cancer biology.
www.biorxiv.org
October 11, 2024 at 12:48 PM
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Analysis of Factors Determining Success in FFPE Based NGS Panel Testing For Lung & Ovarian Cancer https://www.medrxiv.org/content/10.1101/2024.07.29.24311158v1
Analysis of Factors Determining Success in FFPE Based NGS Panel Testing For Lung & Ovarian Cancer https://www.medrxiv.org/content/10.1101/2024.07.29.24311158v1
The identification of oncogenic variants in both lung and ovarian cancer is central to personalised
www.medrxiv.org
July 30, 2024 at 2:40 AM
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BIOZOL GmbH Dianova Clone TG1 is the first monoclonal #antibody for #IHC detection of #cancer #immunology checkpoint biomarker #TIGIT (Tcell immunoreceptor with Ig & ITIM domains) in standard #FFPE human tissue specimen
www.stratech.co.uk/p...
#diagnostics #histopathology
www.stratech.co.uk/p...
#diagnostics #histopathology
September 17, 2025 at 8:00 AM
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Exciting tech advance 4 cancer research: FFPE-CUTAC enables phenotype queries from archived FFPE tissues. This finds a striking correlation between hypertranscription of histones (but not ribosomal genes) & chromosome arm losses, hence, cancer evolution.
RNA polymerase II at histone genes predicts outcome in human cancer
Genome-wide hypertranscription is common in human cancer and predicts poor prognosis. To understand how hypertranscription might drive cancer, we applied our formalin-fixed paraffin-embedded (FFPE)–cl...
www.science.org
February 22, 2025 at 8:50 AM
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A laser capture microdissection-based method for high-sensitivity transcriptomics from archived FFPE tissue slides with single-cell resolution using LCM-FFPEseq https://www.biorxiv.org/content/10.1101/2025.08.13.669096v1
August 16, 2025 at 5:33 AM
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FFixR: A Machine Learning Framework for Accurate Somatic Mutation Calling from FFPE RNA-Seq Data in Cancer
doi.org/10.1101/2025...
Comparison of read mapping and variant calling tools for the analysis of plant NGS data
doi.org/10.1101/2020...
doi.org/10.1101/2025...
Comparison of read mapping and variant calling tools for the analysis of plant NGS data
doi.org/10.1101/2020...
FFixR: A Machine Learning Framework for Accurate Somatic Mutation Calling from FFPE RNA-Seq Data in Cancer
Formalin fixed paraffin embedded (FFPE) tissues are widely used in clinical and research settings, yet their use for detecting somatic mutations from RNA sequencing (RNA seq) is hindered by artefactua...
doi.org
October 18, 2025 at 7:15 AM
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Hey sci bsky, our lab needs to buy FFPE sections from human tumor and we want to be sure we’re working with a reputable biobank. Does anyone have a recommendation or know anything about Accio biobank? Please reskeet and thanks!
October 26, 2023 at 10:29 PM
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A standout aspect of Mann's work is his effort to predict protein expression from FFPE microscopy images. This method could offer a new lens for studying cellular function and pathology.
June 6, 2023 at 5:24 AM
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It definitely works but in our hands has limited depth. DIA with a DDA library (or hybrid library) from fractionated pooled samples usually wins out. Cool to see typical FFPE artefact PTMs abundant in a Fragpipe diaTracer open search though!
June 24, 2025 at 5:33 PM
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