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 9

System / cell line: analysis ✕ Assay: dna-seq ✕ Clear

CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.

PMID 41723172 · PMC13036076 · Nature communications · 2026 · 8 claims · 7 setups

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CRAGE-RB-PI-seq, combining CRAGE genome engineering with randomly-barcoded promoter-library insertion sequencing, enables targeted amplification of barcoded bacterial transcripts that bypasses plant RNA interference.

pseudomonas arabidopsis targeted pi-seq conventional
Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

PMID 26618080 · PMC4655093 · PeerJ · 2015 · 8 claims · 8 setups

Has reproduction · 68

Siphonophorae is the first diverging clade within Hydroidolina.

hydroidolinan nanomia liriope assembled long-range rna-seq dna-seq
Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing.

PMID 34576874 · PMC8467633 · Microorganisms · 2021 · 7 claims · 7 setups

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Amitosis causes random assortment of somatic alleles (IESs) in the highly polyploid Paramecium macronucleus, which can be tracked without phenotypic markers using scDNA-seq.

paramecium tetraurelia telomere-capped simulated single-cell bulk bias
Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

Has reproduction · 91

An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

gossypium longicalyx nine diploids whole-genome wgs read
Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

PMID 36543858 · PMC9772385 · Communications biology · 2022 · 8 claims · 7 setups

Has reproduction · 100

Compiled the largest human embryonic A-to-I editome to date from 2071 RNA-seq transcriptomes and identified thousands of per-stage Recurrent Embryonic Edits (REEs, present in ≥50% of samples per stage)

preimplantation single uniparental embryos rna-seq paired gene
Genomic instability and mono-parental expression mitigate genomic shock in a cross-subgenus Leishmania hybrid.

PMID 41918820 · PMC13034039 · NAR molecular medicine · 2026 · 7 claims · 8 setups

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An in vitro cross between L. infantum and L. tarentolae produced a viable inter-subgenus hybrid, demonstrating genomic compatibility between highly divergent Leishmania species.

infantum linf-gfp bone bmdms genetic flow morphological
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
NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.

PMID 41608734 · PMC12838523 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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NGSTroubleFinder detects cross-sample contamination, sample swaps, kinship, and sex mismatches from BAM/CRAM files without requiring additional variant-calling steps

genomes 1000gp internal whole-genome whole-transcriptome wgs
A haplotype-complete chromosome-level assembly of octoploid Urochloa humidicola cv. Tully reveals multiple genomic compositions and evolutionary histories in the species.

PMID 41678351 · PMC13042314 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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A haplotype-complete, chromosome-level genome assembly of octoploid U. humidicola cv. Tully was generated from PacBio HiFi reads alone

humidicola chromosomes urochloa additional pacbio busco proteome

Experiments

CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.

Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing.

Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

Genomic instability and mono-parental expression mitigate genomic shock in a cross-subgenus Leishmania hybrid.

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

NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.

A haplotype-complete chromosome-level assembly of octoploid Urochloa humidicola cv. Tully reveals multiple genomic compositions and evolutionary histories in the species.