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Method: FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples
- Jeffery M. Vahrenkamp,
- Kathryn Szczotka,
- Mark K. Dodson,
- Elke A. Jarboe,
- Andrew P. Soisson,
- and Jason Gertz
Genome Res. November 2019 29: 1826-1835; Published in Advance October 24, 2019, doi:10.1101/gr.249656.119
..., University of Utah, Salt Lake City, Utah 84112, USA; 3Department of Pathology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA Corresponding author: jay.gertz@hci.utah.eduAbstractThe majority of clinical cancer specimens are preserved as formalin-fixed paraffin-embedded (FFPE...
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Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
- Maria Grazia Mendoza-Ferri,
- Gwendoline Lozachmeur,
- Maximilien Duvina,
- Laetitia Perret,
- Didier Merciris,
- Anne Gigout,
- and Marco Antonio Mendoza-Parra
Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
...related to the resolution of these technologies, their capacity to access to other type of molecular readouts (e.g., chromatin accessibility, epigenetics), their technical limitations resulting from the way in which the biological specimens were preserved (formalin-fixed paraffin-embedded [FFPE] vs. fresh...
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Method: Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors
- Shelsa S. Marcel,
- Austin L. Quimby,
- Melodie P. Noel,
- Oscar C. Jaimes,
- Marjan Mehrab-Mohseni,
- Suud A. Ashur,
- Brian Velasco,
- James K. Tsuruta,
- Sandeep K. Kasoji,
- Charlene M. Santos,
- Paul A. Dayton,
- Joel S. Parker,
- Ian J. Davis,
- and Samantha G. Pattenden
Genome Res. December 2021 31: 2327-2339; Published in Advance November 23, 2021, doi:10.1101/gr.275219.121
...accessibility assays are ineffective for archival formalin-fixed, paraffin-embedded (FFPE) tissues. We have developed a method to efficiently extract intact chromatin from archival tissue via enhanced cavitation with a nanodroplet reagent consisting of a lipid shell with a liquid perfluorocarbon core. Inclusion...
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Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
- Stephanie M. Zimmerman,
- Robin Fropf,
- Bridget R. Kulasekara,
- Maddy Griswold,
- Oliver Appelbe,
- Arya Bahrami,
- Rich Boykin,
- Derek L. Buhr,
- Kit Fuhrman,
- Margaret L. Hoang,
- Quoc Huynh,
- Lesley Isgur,
- Andrew Klock,
- Alecksandr Kutchma,
- Alexa E. Lasley,
- Yan Liang,
- Jill McKay-Fleisch,
- Jeffrey S. Nelson,
- Karen Nguyen,
- Erin Piazza,
- Aric Rininger,
- Daniel R. Zollinger,
- Michael Rhodes,
- and Joseph M. Beechem
Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
...the consequences of this design choice by comparing human WTA with a smaller probe pool targeting 1812 human genes with five probes per target. In matched 200 μm AOIs in formalin-fixed paraffin embedded (FFPE) tonsil tissue, counts from the single WTA probe were well correlated to the mean count of the five probes...
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Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
- Kimberly N. Griffin,
- Benjamin William Walters,
- Haixin Li,
- Huafeng Wang,
- Giulia Biancon,
- Toma Tebaldi,
- Carolyn B. Kaya,
- Jean Kanyo,
- TuKiet T. Lam,
- Andy L. Cox,
- Stephanie Halene,
- Jean-Ju Chung,
- and Bluma J. Lesch
Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
...in vivo using spermatogenic cells as a model. We find that AGO2 transiently binds both chromatin and nucleus-specific mRNA transcripts of hundreds of genes required for sperm production during male meiosis in mice, and that germline conditional knockout (cKO) of Ago2 causes depletion of the encoded...
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Research: Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects
- Jeremy M. Simon,
- Kathryn E. Hacker,
- Darshan Singh,
- A. Rose Brannon,
- Joel S. Parker,
- Matthew Weiser,
- Thai H. Ho,
- Pei-Fen Kuan,
- Eric Jonasch,
- Terrence S. Furey,
- Jan F. Prins,
- Jason D. Lieb,
- W. Kimryn Rathmell,
- and Ian J. Davis
Genome Res. February 2014 24: 241-250; Published in Advance October 24, 2013, doi:10.1101/gr.158253.113
...microarray construction and immunohistochemistry Tissue microarrays (TMAs) were constructed from formalin-fixed, paraffin-embedded tumor blocks from 69 ccRCC tumors and 11 matched normal kidneys collected at the time of nephrectomy. Hematoxylin and eosin–stained slides were reviewed to identify a target area...
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Research: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
- Gary C. Hon,
- R. David Hawkins,
- Otavia L. Caballero,
- Christine Lo,
- Ryan Lister,
- Mattia Pelizzola,
- Armand Valsesia,
- Zhen Ye,
- Samantha Kuan,
- Lee E. Edsall,
- Anamaria Aranha Camargo,
- Brian J. Stevenson,
- Joseph R. Ecker,
- Vineet Bafna,
- Robert L. Strausberg,
- Andrew J. Simpson,
- and Bing Ren
Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
...Diego, La Jolla, California 92093, USA AbstractWhile genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic mutations...
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Research: Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways
- Sanchari Bhattacharyya,
- Kith Pradhan,
- Nathaniel Campbell,
- Jozef Mazdo,
- Aparna Vasantkumar,
- Shahina Maqbool,
- Tushar D. Bhagat,
- Sonal Gupta,
- Masako Suzuki,
- Yiting Yu,
- John M. Greally,
- Ulrich Steidl,
- James Bradner,
- Meelad Dawlaty,
- Lucy Godley,
- Anirban Maitra,
- and Amit Verma
Genome Res. November 2017 27: 1830-1842; Published in Advance October 6, 2017, doi:10.1101/gr.222794.117
...(Applied Biosystems) with randomprimers. qRTPCR was performed using Fast SYBR Green Master Mix (Applied Biosystems Cat. 4385612) and primers specific to MYC. GUSB was used as an internal loading control. Ki67 immunohistochemistry Immunohistochemistry was performed on formalin-fixed paraffin-embedded tissue...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
..., detecting approximately 170,000 unique molecular identifiers (UMIs) and 8600 genes (illumination diameter = 100 µm). Moreover, PCL-seq is compatible with formalin-fixed paraffin-embedded (FFPE) tissues, successfully identifying thousands of differentially enriched transcripts in the digits and vertebrae...
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Research: Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder
- Przemyslaw Szafranski,
- Avinash V. Dharmadhikari,
- Erwin Brosens,
- Priyatansh Gurha,
- Katarzyna E. Kołodziejska,
- Ou Zhishuo,
- Piotr Dittwald,
- Tadeusz Majewski,
- K. Naga Mohan,
- Bo Chen,
- Richard E. Person,
- Dick Tibboel,
- Annelies de Klein,
- Jason Pinner,
- Maya Chopra,
- Girvan Malcolm,
- Gregory Peters,
- Susan Arbuckle,
- Sixto F. Guiang III,
- Virginia A. Hustead,
- Jose Jessurun,
- Russel Hirsch,
- David P. Witte,
- Isabelle Maystadt,
- Neil Sebire,
- Richard Fisher,
- Claire Langston,
- Partha Sen,
- and Paweł Stankiewicz
Genome Res. January 2013 23: 23-33; Published in Advance October 3, 2012, doi:10.1101/gr.141887.112
...). During the last 10 years, we ascertained ACD/MPV samples (mainly formalin-fixed paraffin-embedded lung tissues) from more than 90 families. In 2009, we reported genomic deletions and inactivating point mutations in the FOXF1 gene in chromosome 16q24.1 in unrelated patients with sporadic...

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