ArticleGenome research2019
FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed.
- Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.Journal of translational medicine · 2025Article
- Intra-promoter switch of transcription initiation sites in proliferation signaling-dependent RNA metabolism.Nature structural & molecular biology · 2023Article
- Affordable, accurate and unbiased RNA sequencing by manual library miniaturization: A case study in barley.Plant biotechnology journal · 2023Article
- A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers.Nature biotechnology · 2022Article
- Single-Cell RNA Sequencing with Spatial Transcriptomics of Cancer Tissues.International journal of molecular sciences · 2022Review
- Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues.BMC genomics · 2021Article
- A novel DNA damage response signature of IDH-mutant grade II and grade III astrocytoma at transcriptional level.Journal of cancer research and clinical oncology · 2020Article
- The Application of Single-Cell RNA Sequencing in Vaccinology.Journal of immunology research · 2020Review
- Changing Technologies of RNA Sequencing and Their Applications in Clinical Oncology.Frontiers in oncology · 2020Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The majority of clinical cancer specimens are preserved as formalin-fixed paraffin-embedded (FFPE) samples. For clinical molecular tests to have wide-reaching impact, they must be applicable to FFPE material. Accurate quantitative measurements of RNA derived from FFPE specimens is challenging because of low yields and high amounts of degradation. Here, we present FFPEcap-seq, a method specifically designed for sequencing capped 5' ends of RNA derived from FFPE samples. FFPEcap-seq combines enzymatic enrichment of 5' capped RNAs with template switching to create sequencing libraries. We find that FFPEcap-seq can faithfully capture mRNA expression levels in FFPE specimens while also detecting enhancer RNAs that arise from distal regulatory regions. FFPEcap-seq is a fast and straightforward method for making high-quality 5' end RNA-seq libraries from FFPE-derived RNA.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.