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 14

System / cell line: genome ✕ Assay: integrity ✕ Clear

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 · 7 claims · 6 setups

Has reproduction · 71

Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.

cord maternal genes significant genome pm2.5 isolation
Diversity of tRNA genes in eukaryotes.

PMID 17088292 · PMC1693877 · Nucleic acids research · 2006 · 8 claims · 6 setups

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The number of tRNA genes having the same anticodon but different sequences elsewhere (isodecoder genes) varies significantly (10–246) across 11 eukaryotes despite isoacceptor numbers being similar (41–55)

eukaryotic bacterial genome synthetic genome-wide sequence manual
Comparative analysis of cancer genes in the human and chimpanzee genomes.

PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

chimpanzee non-human cancer comparative pcr targeted
Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

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

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

saliva amplified extracted differentially genome quality extraction
Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

PMID 18803882 · PMC2566316 · BMC genomics · 2008 · 8 claims · 5 setups

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About 20% of the 909,622 SNPs on the SNP Array 6.0 are monomorphic in the Japanese population

genomic japanese reference snp concentration agarose
Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

PMID 34489462 · PMC8421402 · Scientific data · 2021 · 8 claims · 8 setups

Has reproduction · 92

Chromosome-scale genomes of six Leishmaniinae species (five L. (Mundinia) species and one Porcisia species) were sequenced, assembled and annotated, providing genome, proteome, transcriptome and GFF outputs for taxa previously lacking public reference genomes

six same polished each nanopore illumina novo
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

Has reproduction · 86

CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

tissues predicted tss-enhancer cattle cage extraction coexpression
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
Comparative genomics of vertebrate Fox cluster loci.

PMID 17062144 · PMC1634998 · BMC genomics · 2006 · 8 claims · 3 setups

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Two additional human paralogous Fox cluster regions exist, on chromosomes 14 and 20, beyond the previously known chromosome 6 and 16 loci

chimp sequences genomic blast molecular comparative
A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses.

PMID 17997604 · PMC2065879 · PLoS pathogens · 2007 · 8 claims · 5 setups

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Two enJSRV proviruses (enJS56A1 and enJSRV-20) independently acquired a defective, transdominant Gag (R21W substitution) that blocks late replication steps of exogenous JSRV/ENTV

sheep nih3t3 domestic enjsrv bac retroviral locus-specific
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
Analysis of human sarcospan as a candidate gene for CFEOM1.

PMID 11180757 · PMC29083 · BMC genetics · 2001 · 7 claims · 5 setups

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Sarcospan sequence is unmutated in all six CFEOM1 families studied

yac genomic extraocular genome pcr direct immunofluorescence
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

chimpanzee retrofitted primate aspm tar restriction genomic
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 41

Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative

Experiments

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

Diversity of tRNA genes in eukaryotes.

Comparative analysis of cancer genes in the human and chimpanzee genomes.

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

Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

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

Comparative genomics of vertebrate Fox cluster loci.

A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses.

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

Analysis of human sarcospan as a candidate gene for CFEOM1.

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.