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).

• Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

  PMID 18834967 · PMC2561938 · American journal of human genetics · 2008 · 7 claims · 6 setups

  Has reproduction · 70

  Heterozygous CHD7 mutations cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome without the CHARGE phenotype.

  ihh additional chd7 sanger targeted rt-pcr

• Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

  PMID 40233745 · PMC12143324 · Cell genomics · 2025 · 8 claims · 6 setups

  Has reproduction

  SGS is a user-friendly, collaborative, versatile browser for integrative visualization of single-cell and spatial multimodal (scMulti-omics) data

  dorsal hematopoietic brain onek1k sn-m3c-seq scatac-seq spatial

• Single-cell and spatial transcriptomics define 20E-driven developmental reprogramming in silkworm wing disc.

  PMID 41730863 · PMC13039787 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  Wing morphogenesis (Wm) cells act as central progenitors/differentiation hub, giving rise to epithelial and cuticle lineages under lineage-specific transcription factors

  mori spodoptera scrna-seq stereo-seq snrna-seq

• Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.

  PMID 41493197 · PMC13110159 · Plant biotechnology journal · 2026 · 8 claims · 5 setups

  Full-text index only

  An optimised Visium spatial transcriptomics protocol (two-step OCT embedding combined with OCT-Immersion First cryopreservation) preserves high-integrity RNA from fragile plant tissues such as SAM

  maize integrated spatial integrity dimensional

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

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

  Full-text index only

  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

• MultiSP deciphers tissue structure and multicellular communication from spatial multi-omics data.

  PMID 41650976 · PMC13174227 · Cell genomics · 2026 · 7 claims · 5 setups

  Full-text index only

  MultiSP outperforms existing spatial and single-cell multi-omics integration methods in detecting biologically accurate spatial domains across multiple spatial multi-omics technologies and tissue types

  lymph embryo brain postnatal spatial misar-seq chromvar

• Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.

  PMID 41735611 · PMC13095655 · Nature structural & molecular biology · 2026 · 6 claims · 7 setups

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  TADs and large-scale chromatin structures remain largely unchanged during sex determination, suggesting a preformed configuration

  facs-sorted same integrated fgf9 hi-c chip-seq metaloci

• Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

  PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

  Full-text index only

  TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

  myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental

• Spatial gene expression analysis reveals drivers of extremely early lymph node metastasis in breast cancer.

  PMID 41578129 · PMC12932634 · NPJ breast cancer · 2026 · 8 claims · 7 setups

  Full-text index only

  Identified 30 isolated tumor cells (ITCs) in a clinically metastasis-negative tumor-draining lymph node, representing the initial metastatic seeding event, spanning ~200 μm

  dissected same tumor xenium-derived bulk enzymatic whole-genome

• 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

  Full-text index only

  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

• Spatiotemporal dynamics of spermatogenesis: insights from high-resolution spatial transcriptomics and pseudotime trajectories in mouse testes.

  PMID 41602862 · PMC12832764 · Frontiers in reproductive health · 2025 · 8 claims · 7 setups

  Full-text index only

  Salus-STS (1 μm resolution) combined with the Salus Cellbins Algorithm enables accurate subcellular segmentation of individual testicular cells in dense tissue

  testicular testis seminiferous top high-resolution integration pseudotime

• Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.

  PMID 41547856 · PMC12917120 · Nature communications · 2026 · 8 claims · 8 setups

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  GARDEN identifies and characterizes rare pathogenic cell populations/regions in spatial omics by embedding graph-based dynamic attention into a spatially-aware graph fusion contrastive model

  breast anterior brain olfactory 10x starmap slide-seqv2

• 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

• 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

  Full-text index only

  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

• A muscle-centered hierarchical breakdown underlies flight loss during silkworm domestication.

  PMID 41716997 · PMC12915254 · iScience · 2026 · 8 claims · 8 setups

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  Flight loss in B. mori results from a muscle-centered collapse of a three-tiered hierarchical genetic module comprising mitochondrial energy production (COX3/ND1), wing vein patterning (Dally/CtBP), and flight muscle specification (Yki)

  wing wings flight mandarina single-cell spatial velocity

• Spatiotemporal dynamics of ecto-5'-nucleotidase (CD73) in mouse retina under physiological conditions.

  PMID 41560519 · PMC12912271 · Development (Cambridge, England) · 2026 · 8 claims · 6 setups

  Full-text index only

  CD73 expression in the neural retina is restricted to the rod-photoreceptor lineage and becomes robustly detectable from postnatal day (P) 3 onward, persisting into adulthood.

  cd73-bac-egfp cd73-creert2 scrna-seq cd73-knockout immunofluorescence genetic whole-mount

• Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

  PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

  Has reproduction · 85

  High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

  breast er+ epithelial malignant scrna-seq spatial copy

• Single-Cell Transcriptomic Atlases of Camels and Cattle Unravel Molecular Evolution of Digestive and Metabolic Systems.

  PMID 41632085 · PMC13067795 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 7 setups

  Full-text index only

  Generated single-cell/nucleus transcriptomic atlases of camels and cattle across 54 tissues, identifying 124 cell types (78 in camels, 106 in cattle, 59 shared)

  camel bovine structural orthologous scrna-seq spatial scenic

• An in vivo and in vitro spatiotemporal profile of human midbrain development.

  PMID 41633979 · PMC12877092 · Nature communications · 2026 · 8 claims · 6 setups

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  By 22 post-conceptional weeks (PCW), fetal ventral midbrain tissue exhibits structural complexity comparable to adult tissue

  fetal ipsc-derived dopamine immunohistochemistry immunofluorescence droplet-based

• 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