ArticleGenome biology2021
PEPPRO: quality control and processing of nascent RNA profiling data.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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.
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Who cites it
18 citing papers in PubMed.
- Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate.Nucleic acids research · 2026Article
- Evolution of promoter-proximal pausing enabled a new layer of transcription control.Nature structural & molecular biology · 2026Article
- Hypoxia leads to reduced mito-nuclear gene expression and increased mtDNA transcriptional pausing in human cells.Communications biology · 2026Article
- PRMT5 activity sustains histone production to maintain genome integrity.bioRxiv : the preprint server for biology · 2025Article
- Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.BMC genomics · 2025Article
- ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes.Nucleic acids research · 2025Article
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- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- Landscape of enhancer disruption and functional screen in melanoma cells.Genome biology · 2023Article
- Cohesin regulates alternative splicing.Science advances · 2023Article
- Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei.BMC genomics · 2022Article
- Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries.BMC genomics · 2022Article
- Prediction of histone post-translational modification patterns based on nascent transcription data.Nature genetics · 2022Article
- High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma.Frontiers in cell and developmental biology · 2022Article
- Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.GigaScience · 2021Article
- PEPPRO: quality control and processing of nascent RNA profiling data.Genome biology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Nascent RNA profiling is growing in popularity; however, there is no standard analysis pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a comprehensive, scalable workflow for GRO-seq, PRO-seq, and ChRO-seq data. PEPPRO produces uniformly processed output files for downstream analysis and assesses adapter abundance, RNA integrity, library complexity, nascent RNA purity, and run-on efficiency. PEPPRO is restartable and fault-tolerant, records copious logs, and provides a web-based project report. PEPPRO can be run locally or using a cluster, providing a portable first step for genomic nascent RNA analysis.
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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.