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 41

System / cell line: seq ✕ Assay: snrna-seq ✕ Clear

Transcription and potential functions of a novel XIST isoform in male peripheral glia.

PMID 41386982 · PMC12863056 · Genome research · 2026 · 8 claims · 8 setups

Full-text index only

XIST is robustly expressed in male peripheral glia, particularly nonmyelinating Schwann cells, across human heart and skeletal muscle tissue.

heart skeletal atlas peripheral scrna-seq aggregated scatac-seq
Comparative multi-omic analysis reveals conserved and derived mechanisms of fin and limb regeneration.

PMID 41571662 · PMC12923738 · Nature communications · 2026 · 8 claims · 8 setups

Full-text index only

Fin and limb regeneration share conserved proximal and distal blastema territory markers, DNA damage repair activation, hif1a-mediated hypoxia response, and sequential pro-/anti-inflammatory gene programs.

polypterus axolotl zebrafish regenerating single-nucleus spatial single-cell
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
Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.

PMID 41253754 · PMC12627582 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 10

Gli1+ fetal cells are the precursors of postnatal long-lived chondroprogenitors (LLCPs) in the growth plate

fetal left-cart-p21 gli1-creer cartilage single-nuclei scenic bulk
Mouse placentae generated by in vitro fertilization exhibit altered gene expression, activated hypoxia responses, and reduced fitness†.

PMID 40874534 · PMC12808545 · Biology of reproduction · 2026 · 6 claims · 6 setups

Full-text index only

IVF-conceived mouse placentae exhibit global and cell type–specific gene expression differences compared to FB placentae

e12.5 differentially trophoblast placenta single-nucleus pseudobulk pathway
Integrative transcriptome-wide association analyses reveal PRKCG-linked GABAergic dysfunction in Fragile X-associated tremor/ataxia syndrome.

PMID 41507195 · PMC12881518 · Nature communications · 2026 · 8 claims · 8 setups

Full-text index only

A multi-omics strategy combined with TWAS reveals brain-region-specific molecular signatures and striking gene dysregulation concentrated in inhibitory neurons in an FXTAS mouse model.

brain prefrontal pfc gabaergic bulk single-nuclei immunofluorescent
Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 8 setups

Has reproduction · 75

CLAD exhibits specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

clad covid-19 million formalin-fixed single-cell single-nucleus integrated
Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

PMID 41564862 · PMC12866174 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

Full-text index only

A 19-factor cancer-immunoinstructive secretory signature (CISS) is present across multiple human cancers and correlates with pro-tumorigenic tumor microenvironments and poor patient survival.

pancreatic kpc pdac tcga-paad rna-seq bulk proteomics
Aberrant mRNA splicing and impaired hippocampal neurogenesis in Grin2b mutant mice.

PMID 41675057 · PMC12886552 · iScience · 2026 · 8 claims · 6 setups

Full-text index only

Grin2b+/C456Y mice show large-scale, age-dependent brain transcriptomic changes, peaking at 4 weeks postnatally

brain hippocampus neuronal bulk trade gene
Dopamine enhances surface glial glycolysis via acetylcholine and insulin/insulin-like growth factor signaling in the honeybee.

PMID 41797926 · PMC12964235 · iScience · 2026 · 8 claims · 5 setups

Full-text index only

Bromocriptine (dopamine receptor agonist) increases glycolytic flux in forager bee brains

forager targeted qpcr single-cell
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

Full-text index only

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

renal kidney pbmc heart scrna-seq snrna-seq snatac-seq
Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment.

PMID 41556506 · PMC12818872 · eLife · 2026 · 8 claims · 8 setups

Full-text index only

Mouse TM contains three molecularly distinct, reproducible cell subtypes (TM1, TM2, TM3) identified by scRNA-seq and validated by IF/ISH

limbal lmx1b scrna-seq snatac-seq immunofluorescence
Single-cell atlas of the developing Down syndrome brain cortex.

PMID 41545595 · PMC13004680 · Nature medicine · 2026 · 8 claims · 8 setups

Full-text index only

RORB/FOXP1-expressing L4-like excitatory neurons are subtype-specifically and dramatically reduced in Down syndrome fetal cortex, especially at later stages (PCW16-20)

fetal excitatory neural humanized single-nucleus immunostaining compositional
Classification of ALS molecular subtypes: a literature review on machine learning applications and their clinical value.

PMID 41731547 · PMC13037183 · BMC medicine · 2026 · 8 claims · 5 setups

Full-text index only

Unsupervised ML analysis of ALS transcriptomes consistently identifies molecular subtypes reflecting distinct biological processes, primarily oxidative stress (ALS-Ox) and glial activation/neuroinflammation (ALS-Glia), found in every study reviewed.

post-mortem peripheral bulk rna-seq blood
Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs.

PMID 41673768 · PMC12998334 · Journal of experimental & clinical cancer research : CR · 2026 · 6 claims · 8 setups

Full-text index only

Organoids derived from malignant effusions of PDAC patients reproducibly generate peritoneal metastases after orthotopic implantation into the pancreas of immunodeficient mice

pdac organoids frozen pdox orthotopic single-nucleus single-cell
Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 8 setups

Has reproduction · 95

Mineralocorticoid effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule cells

kidney live blood snrna-seq snatac-seq bulk
Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

PMID 40849297 · PMC12375038 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 90

Multi-omic profiling (snRNA-seq + spatial transcriptomics) of human sural nerves identifies novel cell type markers (MLIP in mySC; GRIK3, PRIMA1 in nmSC; CXCL14 in periC) not previously described in rodent or human literature

sural peripheral snrna-seq nerve single-nucleus subcellular situ
Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

PMID 41758938 · PMC12947870 · Science advances · 2026 · 8 claims · 8 setups

Has reproduction · 84

MYOD1 L122R-mutant SRMS tumors contain three coexisting, conserved cell states (progenitor, transition, differentiated) reflecting aberrant myogenic differentiation

patient-derived tumor single paired single-nucleus infercnv aracne-ap
Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.

PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups

Has reproduction · 93

snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.

interscapular ibat bat single-nucleus qpcr western
Single-nucleus RNA sequencing identifies a novel tenogenic heterologous differentiation in endometrial carcinosarcomas: implications for diagnosis and tumor classification.

PMID 41537454 · PMC12805614 · The Journal of pathology · 2026 · 6 claims · 7 setups

Full-text index only

snRNA-seq identifies a novel tenogenic heterologous differentiation program (SCX, MKX, TNMD) in an endometrial carcinosarcoma

ffpe sections tumor cs4 single-nucleus immunohistochemistry fluorescence

Experiments

Transcription and potential functions of a novel XIST isoform in male peripheral glia.

Comparative multi-omic analysis reveals conserved and derived mechanisms of fin and limb regeneration.

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

Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.

Mouse placentae generated by in vitro fertilization exhibit altered gene expression, activated hypoxia responses, and reduced fitness†.

Integrative transcriptome-wide association analyses reveal PRKCG-linked GABAergic dysfunction in Fragile X-associated tremor/ataxia syndrome.

Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

Aberrant mRNA splicing and impaired hippocampal neurogenesis in Grin2b mutant mice.

Dopamine enhances surface glial glycolysis via acetylcholine and insulin/insulin-like growth factor signaling in the honeybee.

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

Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment.

Single-cell atlas of the developing Down syndrome brain cortex.

Classification of ALS molecular subtypes: a literature review on machine learning applications and their clinical value.

Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs.

Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.

Single-nucleus RNA sequencing identifies a novel tenogenic heterologous differentiation in endometrial carcinosarcomas: implications for diagnosis and tumor classification.