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 · 78
annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.
PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups
annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.
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The RNA-binding protein SRSF3 controls epicardial formation by regulating splicing and proliferation.
PMID 41601313 · PMC13006530 · Development (Cambridge, England) · 2026 · 8 claims · 8 setups
SRSF3 is highly expressed in the proepicardial organ and early epicardium, declining after E11.5 and remaining low postnatally
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SETDB1 enables development beyond cleavage stages by extinguishing the MERVL-driven two-cell totipotency transcriptional program in the mouse embryo.
PMID 41697236 · PMC12908936 · eLife · 2026 · 8 claims · 5 setups
Maternal SETDB1 is required for mouse preimplantation development beyond the eight-cell stage
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Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis.
PMID 41781333 · PMC7619044 · Genome research · 2026 · 8 claims · 8 setups
There are few endoderm-specific CRMs; many CRMs governing pancreas development also likely act within the nervous system
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MiR-21-5p Protects Embryonic Growth and Heart Function During Developmental Hypoxia by Dampening HIF Responses and Altering Gene Expression.
PMID 42138560 · PMC13178401 · Comprehensive Physiology · 2026 · 8 claims · 7 setups
Hypoxia induces widespread transcriptomic remodeling in neonatal rat cardiomyocytes (385 DEGs vs normoxia)
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Has reproduction · 65
Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider.
PMID 36203191 · PMC9535882 · BMC biology · 2022 · 8 claims · 8 setups
Comparative RNA-seq of cells isolated from central, intermediate, and peripheral regions of stage-3 embryos identifies genes with locally restricted expression genome-wide
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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 · 59
De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean.
PMID 24586345 · PMC3929608 · PloS one · 2014 · 8 claims · 8 setups
A de novo transcriptome for Calanus finmarchicus was assembled from six developmental-stage libraries, yielding 206,041 contigs and a reference set of 96,090 unique comps, representing a new molecular resource for this species.
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Has reproduction · 71
A global change in RNA polymerase II pausing during the Drosophila midblastula transition.
PMID 23951546 · PMC3743134 · eLife · 2013 · 8 claims · 8 setups
Massive de novo recruitment of Pol II (and TBP) with widespread pausing occurs during the Drosophila midblastula transition, at 4007 promoters (~one third of all genes).
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Has reproduction · 67
Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.
PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups
Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.
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Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.
PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups
A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.
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Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.
PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups
Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster
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miR-203 facilitates timely cell fate transitions via epigenetic modulation during early embryogenesis.
PMID 41811946 · PMC12978216 · Science advances · 2026 · 8 claims · 8 setups
miR-203 is required for a timely totipotency-to-pluripotency transition during early mouse embryogenesis
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Shaken not stirred: a global research cocktail served in Hinxton.
PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups
Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process
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Systems biology of gene regulation fulfills its promise.
PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups
Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.