Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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Has reproduction · 70
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).
PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups
AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella
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Has reproduction · 62
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.
PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups
Inter-specific differences in vertical distribution/microhabitat preference are associated with distinct dynamics of gene expression during dehydration and rehydration phases
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Has reproduction · 73
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.
PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups
De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp
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Has reproduction · 27
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups
A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.
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A transcriptome sequence dataset characterizing eggs, nymphs and adults of Oxycarenus hyalinipennis, the cotton seed bug.
PMID 41717652 · PMC12915258 · Data in brief · 2026 · 8 claims · 8 setups
This dataset provides the first transcriptomic resources for the invasive pest Oxycarenus hyalinipennis
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Has reproduction · 93
A comparison of the large-scale gene expression patterns in summer and fall migratory Pantala flavescens (Fabricius) in northern China.
PMID 39108562 · PMC11301579 · Ecology and evolution · 2024 · 8 claims · 4 setups
624 differentially expressed genes (DEGs) were identified between summer (M7) and fall (M10) migratory P. flavescens
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Has reproduction · 80
Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.
PMID 40680064 · PMC12322963 · Journal of proteome research · 2025 · 8 claims · 7 setups
928 differentially accumulating mRNAs (564 up, 364 down) were identified between exponential and stationary phase
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Has reproduction · 87
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.
PMID 34072576 · PMC8227486 · Genes · 2021 · 7 claims · 8 setups
A new consensus transcriptome of E. gracilis was assembled by combining reads from five independent RNA-seq studies (23 samples)
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Has reproduction · 50
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.
PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups
A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.
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Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.
PMID 41482730 · PMC12958822 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups
O. stricta genome assembly is chromosome-scale, 436 Mb, spanning 12 chromosomes across 2 subgenomes
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Has reproduction · 94
BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.
PMID 35704392 · PMC9546494 · The Plant journal : for cell and molecular biology · 2022 · 8 claims · 6 setups
BaRTv2.18 is the most comprehensive and resolved reference transcriptome in barley to date, containing 39,434 genes and 148,260 transcripts
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Has reproduction · 98
Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm.
PMID 33295865 · PMC8116671 · Microbial genomics · 2020 · 8 claims · 4 setups
wCtub and wDcau (863 988 bp and 863 427 bp) are the smallest Wolbachia genomes sequenced to date and are the first genomes representing supergroup J.
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.
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Has reproduction · 84
The seeker R package: simplified fetching and processing of transcriptome data.
PMID 36389425 · PMC9648347 · PeerJ · 2022 · 8 claims · 4 setups
seeker is an R package that wraps existing tools to fetch and process RNA-seq and microarray data, providing a standard interface, simple parallelization, and detailed logging
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Has reproduction · 57
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.
PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups
ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads
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Has reproduction · 82
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.
PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups
An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.
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Has reproduction · 67
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.
PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups
Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.
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Has reproduction · 90
PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.
PMID 24747190 · PMC4411361 · Genomics, proteomics & bioinformatics · 2014 · 8 claims · 3 setups
PrimerSeq is a user-friendly stand-alone software with a GUI for systematic design and visualization of RT-PCR primers for alternative splicing analysis using user-provided RNA-seq data.
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Has reproduction · 84
The SARS-CoV-2 subgenome landscape and its novel regulatory features.
PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups
Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events
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Has reproduction · 85
An extensive evaluation of read trimming effects on Illumina NGS data analysis.
PMID 24376861 · PMC3871669 · PloS one · 2013 · 8 claims · 8 setups
Read trimming increases the quality and reliability of downstream NGS analyses (RNA-Seq mapping, SNP identification, genome assembly) while reducing execution time and computational resources.