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 13

System / cell line: gene-expression ✕ Assay: integrity ✕ Clear

Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 5 setups

Has reproduction

Expression stability in CHO cell lines is controlled at three levels: choice of integration site, transgene integrity/concatemerization pattern, and stress-related cellular processes.

horizon same cho genome rna-seq targeted
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
Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow.

PMID 35726533 · PMC9542029 · Molecular ecology · 2022 · 7 claims · 8 setups

Has reproduction · 93

Italian sparrow testis exhibits extensive transgressive gene expression relative to both parental species

testis ovary house differentially bulk gene protein-protein
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

Has reproduction · 86

RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

ccds glioblastoma experimental simulated simulated bulk quality
Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

Full-text index only

277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

umbilical ucb zebrafish microarray fluorescence-activated quantitative
Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

Full-text index only

Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

saliva amplified extracted differentially genome quality extraction
Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

PMID 12962547 · PMC212256 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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RMA-generated gene expression values are markedly less variable and more reliable than MAS5.0- and MBEI-derived values

postmortem oligonucleotide real-time quality
Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 8 claims · 6 setups

Has reproduction · 71

Gestational PM2.5 exposure is associated with sex-specific transcriptome signatures in cord blood, with a significant sex-by-exposure interaction for many genes.

cord maternal pm2.5-associated blood whole-genome spatial-temporal overrepresentation
Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

Full-text index only

Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

genomic postmortem nimhgi esr1 targeted case-control family-based
Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

PMID 41876233 · PMC13108381 · The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026 · 8 claims · 5 setups

Has reproduction · 75

Endothelial cell-specific deletion of Adgrl2 impairs cerebrovascular integrity in mice

wild-type cortex brain single-molecule single-cell immunohistochemistry
The butyrophilin 1a1 knockout mouse revisited: Ablation of Btn1a1 leads to concurrent cell death and renewal in the mammary epithelium during lactation.

PMID 34938960 · PMC8664049 · FASEB bioAdvances · 2021 · 8 claims · 8 setups

Has reproduction · 98

BTN1A1 functions as an apical membrane receptor that forms a lipid-droplet secretion complex with the redox enzyme xanthine oxidoreductase (XDH)

mammary rna-seq proteomic qrt-pcr
Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 8 setups

Has reproduction · 78

INVADE-seq (single-cell RNA-seq combined with 16S rRNA targeting) detects a sparse but widespread bacterial presence across diverse testicular cell types

testis young testicular invade-seq histology sperm
Immuno-metabolic dysregulation in type 2 diabetes is associated with altered neutrophil functional plasticity, mitochondrial dysfunction, and compromised responses in sepsis.

PMID 41520116 · PMC12882159 · Journal of translational medicine · 2026 · 8 claims · 8 setups

Full-text index only

Proportions of functionally restricted neutrophil subpopulations (phagocytosis-only vs NETosis-only) are significantly altered in T2D and fail to elicit an immune response upon sepsis induction

peripheral bone plasma neutrophils flow bulk global

Experiments

Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.

Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow.

RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

The butyrophilin 1a1 knockout mouse revisited: Ablation of Btn1a1 leads to concurrent cell death and renewal in the mammary epithelium during lactation.

Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

Immuno-metabolic dysregulation in type 2 diabetes is associated with altered neutrophil functional plasticity, mitochondrial dysfunction, and compromised responses in sepsis.