Search Results - "Paraffin Embedding"

Cryopreserved Tissue Biospecimens Offer Superior Quality for Whole-Genome Sequencing of Various Cancers Compared to Paired Formalin-Fixed Paraffin-Embedded Tissues.

Authors: Dixon K Lee JH Miller R et al.

Source: International journal of molecular sciences [Int J Mol Sci] 2025 Nov 14; Vol. 26 (22). Date of Electronic Publication: 2025 Nov 14.

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

MeSH Terms: Cryopreservation*/methods , Paraffin Embedding*/methods , Neoplasms*/genetics , Neoplasms*/pathology , Whole Genome Sequencing*/methods , Tissue Fixation*/methods, Humans ; Formaldehyde/chemistry ; Mutation

scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.

Authors: Yadav RP Xing P Zhao M et al.

Source: Nature communications [Nat Commun] 2025 Nov 14; Vol. 16 (1), pp. 10022. Date of Electronic Publication: 2025 Nov 14.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

MeSH Terms: Chromatin*/metabolism , Chromatin*/genetics , Paraffin Embedding*/methods , Single-Cell Analysis*/methods , High-Throughput Nucleotide Sequencing*/methods, Humans ; Animals ; Formaldehyde/chemistry ; Mice ; Tissue Fixation/methods ; Transposases/metabolism ; Transposases/genetics ; Epigenesis, Genetic ; Lung Neoplasms/genetics ; Lung Neoplasms/pathology ; Lymph Nodes/pathology ; Lymph Nodes/metabolism ; Spleen ; Lymphoma, Large B-Cell, Diffuse/genetics ; Lymphoma, Large B-Cell, Diffuse/pathology

Optical super-resolution histology of formalin-fixed paraffin-embedded tissue samples: challenges and opportunities.

Authors: Villegas-Hernández LE Dubey VK Acharya G et al.

Source: Nature communications [Nat Commun] 2025 Nov 05; Vol. 16 (1), pp. 9760. Date of Electronic Publication: 2025 Nov 05.

Publication Type: Journal Article; Review

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

MeSH Terms: Paraffin Embedding*/methods , Formaldehyde*/chemistry , Tissue Fixation*/methods , Microscopy*/methods, Humans ; Microscopy, Fluorescence/methods ; Animals ; Single Molecule Imaging/methods

Quantitative proteomics of formalin-fixed, paraffin-embedded cardiac specimens uncovers protein signatures of specialized regions and patient groups.

Authors: Achter JS Jensen THL Pisano P et al.

Source: Nature cardiovascular research [Nat Cardiovasc Res] 2025 Oct; Vol. 4 (10), pp. 1409-1423. Date of Electronic Publication: 2025 Sep 26.

Publication Type: Journal Article

Journal Info: Publisher: Springer Nature Country of Publication: England NLM ID: 9918284280206676 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2731-0590 (Electronic) Linking ISSN: 27310590 NLM ISO Abbreviation: Nat Cardiovasc Res Subsets: MEDLINE

MeSH Terms: Proteomics*/methods , Paraffin Embedding* , Formaldehyde* , Myocardium*/pathology , Myocardium*/metabolism , Myocardium*/chemistry , Tissue Fixation* , Fixatives* , Proteome*, Humans ; Fibrosis ; Biopsy ; Male

Single-nucleus total RNA sequencing of formalin-fixed paraffin-embedded samples using snRandom-seq.

Authors: Xu Z Lyu Y Chen H et al.

Source: Nature protocols [Nat Protoc] 2025 Oct; Vol. 20 (10), pp. 2771-2802. Date of Electronic Publication: 2025 Apr 25.

Publication Type: Journal Article; Review

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101284307 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1750-2799 (Electronic) Linking ISSN: 17502799 NLM ISO Abbreviation: Nat Protoc Subsets: MEDLINE

MeSH Terms: Paraffin Embedding*/methods , Sequence Analysis, RNA*/methods , RNA, Small Nuclear*/genetics , Single-Cell Analysis*/methods , Cell Nucleus*/genetics, Formaldehyde/chemistry ; Humans ; Tissue Fixation/methods ; High-Throughput Nucleotide Sequencing/methods

Paraffin sectioning in the modern laboratory and the problem of static electricity: a review.

Authors: Sluys R de Waart S

Source: Journal of histotechnology [J Histotechnol] 2025 Sep; Vol. 48 (3), pp. 117-122. Date of Electronic Publication: 2025 Aug 14.

Publication Type: Review; Editorial

Journal Info: Publisher: Historical Metallurgy Society Country of Publication: England NLM ID: 8003807 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2046-0236 (Electronic) Linking ISSN: 01478885 NLM ISO Abbreviation: J Histotechnol Subsets: MEDLINE

MeSH Terms: Paraffin Embedding*/methods , Paraffin Embedding*/instrumentation , Electricity* , Microtomy*/methods , Microtomy*/instrumentation , Laboratories* , Paraffin*, Humans ; Humidity

Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

Authors: Mucaki EJ Zhang W Saha A et al.

Source: Journal of translational medicine [J Transl Med] 2025 Sep 30; Vol. 23 (1), pp. 1023. Date of Electronic Publication: 2025 Sep 30.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 101190741 Publication Model: Electronic Cited Medium: Internet ISSN: 1479-5876 (Electronic) Linking ISSN: 14795876 NLM ISO Abbreviation: J Transl Med Subsets: MEDLINE

MeSH Terms: Paraffin Embedding* , Formaldehyde*/chemistry , Tissue Fixation* , Gene Expression Profiling* , Transcriptome*/genetics, Humans

[Experimental optimization of paraffin sectioning techniques for the eyeball].

Authors: Huang FF Du MM Gao N et al.

Source: [Zhonghua yan ke za zhi] Chinese journal of ophthalmology [Zhonghua Yan Ke Za Zhi] 2025 Sep 11; Vol. 61 (9), pp. 697-705.

Publication Type: English Abstract; Journal Article

Journal Info: Publisher: Chinese Medical Association Country of Publication: China NLM ID: 16210540R Publication Model: Print Cited Medium: Print ISSN: 0412-4081 (Print) Linking ISSN: 04124081 NLM ISO Abbreviation: Zhonghua Yan Ke Za Zhi Subsets: MEDLINE

MeSH Terms: Paraffin Embedding*/methods , Eye*/anatomy & histology, Animals ; Swine ; Humans ; Tissue Fixation/methods ; Male ; Fixatives ; Formaldehyde

High-Throughput Proteomic and Phosphoproteomic Analysis of Formalin-Fixed Paraffin-Embedded Tissues.

Authors: Haines M Thorup JR Gohsman S et al.

Source: Molecular & cellular proteomics : MCP [Mol Cell Proteomics] 2025 Sep; Vol. 24 (9), pp. 101044. Date of Electronic Publication: 2025 Jul 29.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Inc. on behalf of American Society for Biochemistry and Molecular Biology Country of Publication: United States NLM ID: 101125647 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-9484 (Electronic) Linking ISSN: 15359476 NLM ISO Abbreviation: Mol Cell Proteomics Subsets: MEDLINE

MeSH Terms: Proteomics*/methods , Paraffin Embedding* , Phosphoproteins*/metabolism , Proteome*, Humans ; Formaldehyde/chemistry ; Tissue Fixation ; Lung Neoplasms/metabolism ; Lung Neoplasms/pathology ; Tandem Mass Spectrometry ; Adenocarcinoma of Lung/metabolism ; Chromatography, Liquid

Comparative analysis of library preparation approaches for FFPE gene expression profiling and related recommendations.

Authors: Pignatta S Tazzari M Indio V et al.

Source: Scientific reports [Sci Rep] 2025 Aug 12; Vol. 15 (1), pp. 29592. Date of Electronic Publication: 2025 Aug 12.

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH Terms: Gene Library* , Gene Expression Profiling*/methods , Paraffin Embedding*/methods, Humans ; High-Throughput Nucleotide Sequencing/methods ; Tissue Fixation/methods ; Formaldehyde/chemistry ; Sequence Analysis, RNA/methods ; Transcriptome ; Exome Sequencing ; RNA-Seq/methods

A nanoscale quality control framework for assessing FFPE DNA integrity in cancer research.

Authors: Huang Z Si Y Zhang Y et al.

Source: Nanoscale horizons [Nanoscale Horiz] 2025 Jul 21; Vol. 10 (8), pp. 1692-1702. Date of Electronic Publication: 2025 Jul 21.

Publication Type: Journal Article

Journal Info: Publisher: Royal Society of Chemistry Country of Publication: England NLM ID: 101712576 Publication Model: Electronic Cited Medium: Internet ISSN: 2055-6764 (Electronic) Linking ISSN: 20556756 NLM ISO Abbreviation: Nanoscale Horiz Subsets: MEDLINE

MeSH Terms: Paraffin Embedding* , DNA*/genetics , Neoplasms*/genetics, Humans ; Quality Control ; Formaldehyde/chemistry ; Tissue Fixation ; Female ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide ; Endometrial Neoplasms/genetics ; DNA Fragmentation

μMap-FFPE: A High-Resolution Protein Proximity Labeling Platform for Formalin-Fixed Paraffin-Embedded Tissue Samples.

Authors: Bissonnette NB Zamanis ME Knutson SD et al.

Source: Journal of the American Chemical Society [J Am Chem Soc] 2025 Jul 09; Vol. 147 (27), pp. 23387-23394. Date of Electronic Publication: 2025 Jun 25.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 7503056 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-5126 (Electronic) Linking ISSN: 00027863 NLM ISO Abbreviation: J Am Chem Soc Subsets: MEDLINE

MeSH Terms: Formaldehyde*/chemistry , Paraffin Embedding* , Tissue Fixation* , Antigens, CD20*/metabolism , Antigens, CD20*/chemistry , Proteins*, Humans ; Staining and Labeling/methods

Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis.

Authors: Ferrini E Bonfini C Marchese G et al.

Source: Respiratory research [Respir Res] 2025 Jul 02; Vol. 26 (1), pp. 225. Date of Electronic Publication: 2025 Jul 02.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 101090633 Publication Model: Electronic Cited Medium: Internet ISSN: 1465-993X (Electronic) Linking ISSN: 14659921 NLM ISO Abbreviation: Respir Res Subsets: MEDLINE

MeSH Terms: Paraffin Embedding*/methods , Transcriptome* , Pulmonary Fibrosis*/genetics , Pulmonary Fibrosis*/metabolism , Pulmonary Fibrosis*/chemically induced , Pulmonary Fibrosis*/pathology , Lung*/metabolism , Lung*/pathology , Gene Expression Profiling*/methods , Tissue Fixation*/methods , Idiopathic Pulmonary Fibrosis*/genetics , Idiopathic Pulmonary Fibrosis*/pathology , Idiopathic Pulmonary Fibrosis*/metabolism , Idiopathic Pulmonary Fibrosis*/chemically induced, Animals ; Mice ; Mice, Inbred C57BL ; Humans ; Formaldehyde ; Male ; Bleomycin/toxicity ; Disease Models, Animal ; Female

Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues.

Authors: Guo P Chen Y Mao L et al.

Source: Nature communications [Nat Commun] 2025 Jul 01; Vol. 16 (1), pp. 5945. Date of Electronic Publication: 2025 Jul 01.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

MeSH Terms: Chromatin*/metabolism , Chromatin*/genetics , Paraffin Embedding*/methods , Formaldehyde*/chemistry, Animals ; Humans ; Mice ; Melanoma/genetics ; Melanoma/pathology ; Melanoma/metabolism ; Tissue Fixation/methods ; Epigenomics/methods ; Single-Cell Analysis ; Brain/metabolism

Are pre-analytical factors fully considered in forensic FFPE molecular analyses? A systematic review reveals the need for standardised procedures.

Authors: Previderè C Bonin S Cuttaia C et al.

Source: International journal of legal medicine [Int J Legal Med] 2025 Jul; Vol. 139 (4), pp. 1439-1452. Date of Electronic Publication: 2025 Apr 02.

Publication Type: Journal Article; Systematic Review

Journal Info: Publisher: Springer International Country of Publication: Germany NLM ID: 9101456 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1437-1596 (Electronic) Linking ISSN: 09379827 NLM ISO Abbreviation: Int J Legal Med Subsets: MEDLINE

MeSH Terms: Paraffin Embedding* , Tissue Fixation* , DNA*/analysis , RNA*/analysis , Pre-Analytical Phase*/standards, Humans ; Formaldehyde ; Forensic Pathology ; Postmortem Changes ; Specimen Handling/standards ; Autopsy

Formalin-fixed paraffin-embedded (FFPE) samples help to investigate transcriptomic responses in wildlife disease.

Authors: Miller AK Brosnahan CL Pande A et al.

Source: Molecular ecology resources [Mol Ecol Resour] 2025 Jul; Vol. 25 (5), pp. e13805. Date of Electronic Publication: 2023 May 07.

Publication Type: Journal Article

Journal Info: Publisher: Blackwell Country of Publication: England NLM ID: 101465604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1755-0998 (Electronic) Linking ISSN: 1755098X NLM ISO Abbreviation: Mol Ecol Resour Subsets: MEDLINE

MeSH Terms: Paraffin Embedding*/methods , Lampreys*/genetics , Gene Expression Profiling* , Transcriptome* , Tissue Fixation*/methods , Fish Diseases*, Animals ; Formaldehyde ; Animals, Wild ; Host-Pathogen Interactions

Comparative analysis of asbestos body and fiber content in formalin-fixed vs. paraffin-embedded lung tissue.

Authors: Kuhn BK Vrugt B Low A et al.

Source: Frontiers in public health [Front Public Health] 2025 Jun 11; Vol. 13, pp. 1590802. Date of Electronic Publication: 2025 Jun 11 (Print Publication: 2025).

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: Frontiers Editorial Office Country of Publication: Switzerland NLM ID: 101616579 Publication Model: eCollection Cited Medium: Internet ISSN: 2296-2565 (Electronic) Linking ISSN: 22962565 NLM ISO Abbreviation: Front Public Health Subsets: MEDLINE

MeSH Terms: Formaldehyde* , Paraffin Embedding*/methods , Lung*/chemistry , Lung*/pathology , Asbestos*/analysis , Mineral Fibers*/analysis, Humans ; United Kingdom ; Switzerland ; Male ; Occupational Exposure/analysis ; Tissue Fixation/methods ; Asbestos, Amphibole/analysis ; Female ; Middle Aged ; Aged

Examination of paraffin-embedded testes of domestic cats and dogs by light and scanning electron microscopy.

Authors: Kandil B Demirci B Bayraktaroğlu AG et al.

Source: Micron (Oxford, England : 1993) [Micron] 2025 Jun; Vol. 192-193, pp. 103816. Date of Electronic Publication: 2025 Mar 11.

Publication Type: Journal Article

Journal Info: Publisher: Pergamon Press Country of Publication: England NLM ID: 9312850 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-4291 (Electronic) Linking ISSN: 09684328 NLM ISO Abbreviation: Micron Subsets: MEDLINE

MeSH Terms: Testis*/ultrastructure , Testis*/anatomy & histology , Microscopy, Electron, Scanning*/methods , Paraffin Embedding*, Animals ; Male ; Dogs ; Cats ; Seminiferous Tubules/ultrastructure ; Microscopy/methods

NanoCMSer: a consensus molecular subtype stratification tool for fresh-frozen and paraffin-embedded colorectal cancer samples.

Authors: Torang A van de Weerd S Lammers V et al.

Source: Molecular oncology [Mol Oncol] 2025 May; Vol. 19 (5), pp. 1332-1346. Date of Electronic Publication: 2024 Dec 25.

Publication Type: Journal Article

Journal Info: Publisher: John Wiley & Sons, Inc Country of Publication: United States NLM ID: 101308230 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-0261 (Electronic) Linking ISSN: 15747891 NLM ISO Abbreviation: Mol Oncol Subsets: MEDLINE

MeSH Terms: Colorectal Neoplasms*/genetics , Colorectal Neoplasms*/pathology , Colorectal Neoplasms*/classification , Paraffin Embedding*, Humans ; Biomarkers, Tumor/genetics ; Consensus

Dimethyl carbonate replaces xylene in paraffin section as a biosafe and effective transparent reagent.

Authors: Chen X Zou L Tian D et al.

Source: Biotechnic & histochemistry : official publication of the Biological Stain Commission [Biotech Histochem] 2025 May; Vol. 100 (4), pp. 240-255. Date of Electronic Publication: 2025 Apr 28.

Publication Type: Journal Article

Journal Info: Publisher: Taylor & Francis Country of Publication: England NLM ID: 9107378 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1473-7760 (Electronic) Linking ISSN: 10520295 NLM ISO Abbreviation: Biotech Histochem Subsets: MEDLINE

MeSH Terms: Xylenes*/chemistry , Paraffin Embedding*/methods , Paraffin*/chemistry, Animals ; Mice ; Formates