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).

Publications 1.3k Datasets 392.5k Experiments 1.8k

System / cell line: seq ✕ Clear

Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

Has reproduction · 58

Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

dissected concatenated yakuba reference whole-transcriptome novo read
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

Has reproduction · 67

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.

anas duck million random illumina read novo
Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups

Has reproduction · 93

24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).

jatropha geo bulk semi-quantitative quantitative
Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

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RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic
Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.

PMID 38892065 · PMC11172245 · International journal of molecular sciences · 2024 · 8 claims · 8 setups

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HR+/HER2-BC tumor epithelial cells comprise four single-cell-defined functional (SC-f) subtypes: migratory, secretory, proliferating, and dysfunctional.

hr+ epcam-sorted tumor tcga-brca droplet sidr-seq bulk
Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

tcga-luad best brain advanced bulk kaplan-meier pearson
Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature.

PMID 35300606 · PMC8932150 · BMC plant biology · 2022 · 7 claims · 8 setups

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Combined SGS+TGS full-length transcriptome sequencing generated 41,016 high-quality potato transcripts, including 15,189 putative new transcripts

potato pacbio illumina physiological
bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling.

PMID 37028916 · PMC10275263 · RNA (New York, N.Y.) · 2023 · 8 claims · 4 setups

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bakR uses Bayesian hierarchical modeling to share information (specifically a replicate variability vs. read count trend) across transcripts, increasing statistical power for differential kinetic analysis

simulated existing simulated nucleotide
IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.

PMID 25406361 · PMC4274634 · RNA (New York, N.Y.) · 2015 · 8 claims · 6 setups

Has reproduction · 30

Existing ab initio assemblers (Cufflinks, Scripture) annotate at most one 3' boundary per terminal exon and therefore cannot assemble coexpressed tandem 3' UTR isoforms.

mapped simulated rna-seq ict1 computational benchmarking 3'-seq
RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.

PMID 41222189 · PMC12857227 · GigaScience · 2026 · 8 claims · 8 setups

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RNA-SeqEZPZ is the first open-source tool offering a point-and-click interface with interactive plots, spanning raw FASTQ reads through differential gene and pathway analysis.

generic paired-end aligned gene bulk adapter read
Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets.

PMID 41563441 · PMC13007207 · Diabetes · 2026 · 8 claims · 7 setups

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5′ single-cell library preparation protocols outperform 3′ protocols for transcript identification and read length

lines pancreatic spleen dtc single-cell bulk ngs
CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

PMID 41566196 · PMC12895761 · BMC bioinformatics · 2026 · 6 claims · 6 setups

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CRESCENT is a Snakemake workflow performing fully automated, comprehensive RNA-Seq analysis integrating differential expression, differential alternative splicing (DAS), differential transcript usage (DTU), and GO enrichment

arabidopsis bulk rna-seq-based rna-seq
Combinatory differentiation of human induced pluripotent stem cells generates functional thymic epithelium driving dendritic cell and CD4/CD8 T cell development.

PMID 41577697 · PMC12932823 · Nature communications · 2026 · 8 claims · 6 setups

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DOE-based multifactorial screening combined with bulk RNA-seq comparison to scRNA-seq pharyngeal atlases identifies signaling factors that optimize iPSc differentiation toward thymic epithelial progenitors (TEPs)

ipsc embryonic ipsc-derived bulk scrna-seq qpcr
omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

PMID 41582216 · PMC12837286 · Genome biology · 2026 · 8 claims · 6 setups

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omnideconv is an R package providing a unified interface to twelve second-generation deconvolution methods (AutoGeneS, BayesPrism, Bseq-SC, Bisque, CDseq, CIBERSORTx, CPM, DWLS, MOMF, MuSiC, SCDC, Scaden)

blood-derived pbmc blood spleen bulk scrna-seq pseudo-bulk
Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora.

PMID 41612263 · PMC12924552 · BMC biology · 2026 · 8 claims · 6 setups

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Profiling gene expression across 26 life stages of A. millepora and building an interactive Shiny-based tool (DEView) enables comprehensive visualisation of developmental transcriptomic data.

acropora millepora bulk differential pca
CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.

PMID 41630911 · PMC12860730 · iScience · 2026 · 8 claims · 8 setups

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CTCF and cohesin (RAD21) remain co-bound to DNA throughout interphase, including during the S (replication) phase, in HeLa cells

hela tumors flow chromatin frap
Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

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Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

apc-deficient heart ileum fresh-frozen spatial high-resolution bulk
Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing sarcoma.

PMID 41792463 · PMC13084053 · EMBO molecular medicine · 2026 · 7 claims · 8 setups

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Combining cfDNA methylome (EwingSign) and fragmentome analysis detects all clinically confirmed relapse events in EwS/CIC patients

plasma cfdna t7-mbd-seq ichorcna fragment
Resource Availability Modulates Gene Expression Across Life Stages in a Migratory Butterfly.

PMID 41797265 · PMC12968515 · Molecular ecology · 2026 · 7 claims · 6 setups

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Adult female exposure to host plants for egg-laying is associated with differential expression of ecdysteroid and juvenile-hormone pathway genes, consistent with endocrine regulation of reproductive readiness and the oogenesis–flight syndrome

vanessa bulk gene kegg
Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.

PMID 41821037 · PMC12983708 · Genome biology · 2026 · 8 claims · 8 setups

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Horizontal integration of scRNA-seq and snRNA-seq improves cell-type identification

renal kidney pbmc heart scrna-seq snrna-seq snatac-seq

Experiments

Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.

Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature.

bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling.

IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.

RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.

Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets.

CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

Combinatory differentiation of human induced pluripotent stem cells generates functional thymic epithelium driving dendritic cell and CD4/CD8 T cell development.

omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora.

CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.

Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing sarcoma.

Resource Availability Modulates Gene Expression Across Life Stages in a Migratory Butterfly.

Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.