ArticleBMC genomics2019
A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 21 citations in OpenAlex.
- A bone fragment-based protocol for RNA analysis of osteocyte-associated transcripts in surgically obtained human bone specimens.MethodsX · 2026Article
- Messenger RNA From Canine Cytology Lymph Node Specimens Can Be Utilised for Gene Expression Profiling Using Digital RNA Counting.Veterinary and comparative oncology · 2026Article
- Transcriptomes of thirteen healthy feline tissue types.BMC genomics · 2025Article
- Reference-free RNA profiling predicts triple negative breast cancer chemoresistance to neoadjuvant treatment.NAR cancer · 2025Article
- Comparative analysis of library preparation approaches for FFPE gene expression profiling and related recommendations.Scientific reports · 2025Article
- Single-cell transcriptome of mouse hippocampus identifies neural precursor-like cells, and reveals IL15Rα knock out-mediated neuron remodeling.BMC genomics · 2025Article
- Advances in spatial transcriptomics and its application in the musculoskeletal system.Bone research · 2025Review
- Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues.BioTechniques · 2025Article
- Single-Cell Sequencing in Neurodegenerative Disorders.Molecular diagnosis & therapy · 2023Review
- Microisolation of Spatially Characterized Single Populations of Neurons for RNA Sequencing from Mouse and Postmortem Human Brain Tissues.Journal of clinical medicine · 2023Article
- Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples.Nature communications · 2023Article
- Reproducible and sensitive micro-tissue RNA sequencing from formalin-fixed paraffin-embedded tissues for spatial gene expression analysis.Scientific reports · 2022Article
- Whole-Transcriptome Profiling on Small FFPE Samples: Which Sequencing Kit Should Be Used?Current issues in molecular biology · 2022Article
- Chemical capping improves template switching and enhances sequencing of small RNAs.Nucleic acids research · 2022Article
- Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action.Toxicology reports · 2022Article
- Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration.Frontiers in molecular biosciences · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFormalin-fixed and paraffin-embedded (FFPE) blocks held in clinical laboratories are an invaluable resource for clinical research, especially in the era of personalized medicine. It is important to accurately quantitate gene expression with degraded and small amounts of total RNA from FFPE materials.
resultsHigh concordance in transcript quantifications were shown between FF and FFPE samples using the same kit. The gene expression using the TaKaRa kit showed a difference with other kits, which may be due to the different principle of rRNA depletion or the amount of input total RNA. For seriously degraded RNA from FFPE samples, libraries could be constructed with as low as 50 ng of total RNA, although there was residual rRNA in the libraries. Data analysis with HISAT demonstrated that the unique mapping ratio, percentage of exons in unique mapping reads and number of detected genes decreased along with the decreasing quality of input RNA.
conclusionsThe method of RNA library construction with rRNA depletion can be used for clinical FFPE samples. For degraded and low-input RNA samples, it is still possible to obtain repeatable RNA expression profiling but with a low unique mapping ratio and high residual rRNA.
Indexed as
Identifiers
What OpenQuestion holds
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.