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).

• 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

  Has reproduction · 65

  Comparative RNA-seq of cells isolated from central, intermediate, and peripheral regions of stage-3 embryos identifies genes with locally restricted expression genome-wide

  tepidariorum drosophila rna-seq whole-mount parental

• 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

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  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

  c57bl orthologous alpha-defensin defensin manual comparative sequence

• A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

  PMID 17183673 · PMC1762436 · PloS one · 2006 · 8 claims · 7 setups

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  HCNCp is a novel invariant (non-variant) cyst protein belonging to a new family of high-cysteine membrane proteins (HCMp) abundant in the Giardia genome

  giardia serial northern western

• Transcriptomic analysis of the highly derived radial body plan of a sea urchin.

  PMID 24696402 · PMC4007537 · Genome biology and evolution · 2014 · 7 claims · 7 setups

  Has reproduction · 68

  A de novo reference transcriptome for Heliocidaris erythrogramma spanning larval, metamorphic, and postmetamorphic stages provides a genomic resource for studying radial body plan evolution.

  sea heliocidaris panther novo rna-seq principal

• Comprehensive stage- and tissue-specific transcriptome of the global ecosystem service insect, marmalade hoverfly Episyrphus balteatus.

  PMID 41927565 · PMC13216633 · Scientific data · 2026 · 8 claims · 8 setups

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  Generated a comprehensive developmental- and tissue-resolved transcriptome dataset for Episyrphus balteatus as a community resource

  egg larva pupa antenna bulk

• From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.

  PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 88

  Flower bud developmental stages (organogenesis, paradormancy, endodormancy, dormancy release, ecodormancy) are defined by distinct, stage-specific gene expression programs

  flower sweet sequencing differential principal

• Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize.

  PMID 33705553 · PMC8195531 · Plant physiology · 2021 · 8 claims · 4 setups

  Has reproduction · 76

  Increasing maximum daily temperature (MDT) elevates the frequency of alternative splicing in maize leaves, particularly intron retention (IR) and exon skipping (ES).

  maize rna-seq gene differential

• ECgene: genome annotation for alternative splicing.

  PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

  brca2 rgs17 organs cdna genomic genome transcript

• Single-cell analysis reveals multi-faceted features of B cell development, together with age-associated B cell subpopulations.

  PMID 41520091 · PMC12905261 · Communications biology · 2026 · 8 claims · 8 setups

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  18 B cell subpopulations were identified spanning the full developmental continuum from early progenitors to plasma cells, including 4 previously unappreciated minor subpopulations (FTLhi, S100A8hi immature; FOShi, HSPA1Ahi naïve).

  in-house enriched tonsil peripheral scrna-seq scvdj-seq velocity

• Single-cell transcriptomic analysis of plant quiescent center by third-generation sequencing reveals developmental trajectories.

  PMID 41664205 · PMC12990480 · Genome biology · 2026 · 8 claims · 8 setups

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  Developed an improved protoplasting/hand-picking protocol enabling isolation of intact QC cells for single-cell long-read RNA sequencing (SCAN-seq)

  arabidopsis single-cell rt-pcr agarose

• 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

  Has reproduction · 59

  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.

  calanus pooled raw combined bulk extraction read

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative

• Cycloheximide-resistant ribosomes reveal adaptive translation dynamics in C. elegans.

  PMID 40929375 · PMC12477835 · Genetics · 2026 · 8 claims · 8 setups

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  A P55Q substitution in ribosomal protein RPL-36A confers strong resistance to cycloheximide in C. elegans

  elegans crispr-cas9 larval rna-seq

• Prediction of Alzheimer's disease-specific phospholipase c gamma-1 SNV by deep learning-based approach for high-throughput screening.

  PMID 33397809 · PMC7826347 · Proceedings of the National Academy of Sciences of the United States of America · 2021 · 7 claims · 7 setups

  Has reproduction · 48

  An AD-specific frameshift insertion SNV in exon 27 of mouse PLCγ1 causes abnormal exon skipping (exons 26-30) during mRNA maturation in 5xFAD cortex

  cortex forebrain plcγ1 bulk rna-seq-based western

• Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.

  PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 57

  t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes

  calanus same 11k degs bulk dimensionality differential

• Microarray analysis: genome-scale hypothesis scanning.

  PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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  Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

  drosophila yeast diffuse breast microarray integrated gene

• 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

  Has reproduction · 67

  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.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

  PMID 17629917 · PMC1934368 · BMC genomics · 2007 · 8 claims · 5 setups

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  Sea urchins possess 10 SpREJ (PKD1 family) genes, compared to five in humans, all defined by possession of a ~600 residue REJ domain

  strongylocentrotus sprej purpuratus full-length cdna secondary real-time

• Biphasic expression of thyroid hormone receptor TRβ1 in mammalian retina and anterior ocular tissues.

  PMID 37033230 · PMC10076699 · Frontiers in endocrinology · 2023 · 7 claims · 8 setups

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  TRβ1 shows a biphasic, late-peaking expression profile in retina that contrasts with the early embryonic peak of TRβ2

  retina fetal retinal cones rna-seq lacz immunofluorescence

• Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution.

  PMID 41388990 · PMC12776951 · The Plant cell · 2026 · 8 claims · 6 setups

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  MERFISH was successfully optimized for wheat inflorescence tissue, enabling localization of a 200-gene panel to cellular resolution across 4 developmental stages

  microdissected cryosectioned wheat merfish-imaged bulk merfish single-nucleus