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 25

System / cell line: heart ✕ Assay: rt-pcr ✕ Clear

PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

PMID 24747190 · PMC4411361 · Genomics, proteomics & bioinformatics · 2014 · 8 claims · 3 setups

Has reproduction · 90

PrimerSeq is a user-friendly stand-alone software with a GUI for systematic design and visualization of RT-PCR primers for alternative splicing analysis using user-provided RNA-seq data.

heart genome rna-seq rt-pcr
Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

Has reproduction · 64

Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

heart degs dgat2 mitodegs microarray kegg protein-protein
Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

PMID 17480121 · PMC1865561 · PLoS genetics · 2007 · 7 claims · 8 setups

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KLF14 is a novel imprinted gene showing monoallelic maternal expression in embryonic and extra-embryonic tissues of both human and mouse

embryonic fetal monochromosomal fibroblasts allele-specific rt-pcr chromatin
Genetic Dissection of Tissue-Specific Apolipoprotein E Function for Hypercholesterolemia and Diet-Induced Obesity.

PMID 26695075 · PMC4687855 · PloS one · 2015 · 8 claims · 8 setups

Has reproduction

Hepatocyte apoE is required for normal VLDL production and protects against diet-induced dyslipidemia

liver plasma pooled real-time western elisa
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
GENCODE: producing a reference annotation for ENCODE.

PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

tissues encode rt-pcr comparative automated
Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.

PMID 18443592 · PMC2742198 · Nature genetics · 2008 · 8 claims · 8 setups

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Osteoglycin (Ogn) is a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM

heart ogn cos-1 neonatal eqtl quantitative genome-wide
Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

bac heart ccs genomic genomic rt-pcr transcription
Candidate target genes for loss of heterozygosity on human chromosome 17q21.

PMID 15187990 · PMC2409524 · British journal of cancer · 2004 · 8 claims · 5 setups

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JUP (plakoglobin) is the only identified gene physically located between the D17S746 and D17S846 markers that define the smallest common region of LOH on chromosome 17q21

genomic normal breast p1-phage nucleotide rt-pcr cold
GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology.

PMID 16919418 · PMC2842930 · Genomics · 2006 · 8 claims · 8 setups

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Human FXN YAC transgenes containing GAA repeat expansions (YG22, YG8) rescue the embryonic lethality of homozygous Fxn knockout mice

yg22 tissues lysates sciatic breeding semiquantitative western
Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

PMID 16855283 · PMC1524921 · Nucleic acids research · 2006 · 8 claims · 5 setups

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Four novel brain-specific paternally expressed transcripts (BB077283, BM117114, AK080843, AV328498) were identified and validated on proximal Chr 7.

tissues inter-subspecies placenta genomic microarray rt-pcr sequencing
Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

placenta five lines huh7 5'-race rt-pcr real-time
Identification of novel homologous microRNA genes in the rhesus macaque genome.

PMID 18186931 · PMC2254598 · BMC genomics · 2008 · 8 claims · 2 setups

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454 rhesus miRNA genes were identified in total, including 383 novel genes in addition to 71 previously reported

rhesus genome polya
Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

PMID 15804357 · PMC1129089 · BMC genomics · 2005 · 8 claims · 6 setups

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MagT1 is a novel mammalian Mg2+ transporter with channel-like properties, showing no amino acid sequence identity to other known transporters

kidney mdct tissues xenopus oligonucleotide northern real-time
Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

PMID 33722289 · PMC7962346 · Genome biology · 2021 · 6 claims · 7 setups

Has reproduction · 66

A PE2-mediated single-base (C>G) substitution in the Tspan2 CArG box causes cell-specific loss of Tspan2 mRNA in aorta and bladder but not heart or brain, mirroring HDR-mediated 3-bp substitution.

zygotes aorta genomic aortae crispr prime quantitative
52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.

PMID 7561701 · PMC2192297 · The Journal of experimental medicine · 1995 · 7 claims · 7 setups

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The 52-kD SS-A/Ro gene spans 10 kb of DNA and is composed of seven exons, with the translation initiation codon in exon 2 and the leucine zipper encoded by exon 4.

molt-4 placental placenta fetal cdna genomic race
Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

PMID 12783626 · PMC161800 · BMC genomics · 2003 · 8 claims · 5 setups

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A comparative genomics approach using hamster testis cDNA sequencing can identify genes not previously annotated in the human, mouse, rat and Fugu genomes

hamster testis predicted cdna northern comparative
MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene.

PMID 18154640 · PMC2233610 · BMC medical genetics · 2007 · 8 claims · 6 setups

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Chromosome 8p23.1 has previously been proposed as a nuclear modifier locus for A1555G-associated hearing loss phenotype

blood a1555g lymphoblastoid nuclear pcr-rflp direct rt-pcr
Estimation of genetic parameters and genome-wide association study for carcass traits in native chickens.

PMID 40211845 · PMC12229932 · Animal bioscience · 2025 · 7 claims · 5 setups

Has reproduction · 71

311 SNPs and 73 candidate genes (e.g., IGF2BP1, BMP3, ACSL5) are significantly associated with carcass traits in Sanhuang chickens

sanhuang chickens chicken breast whole-genome phenotypic genomic
Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.

PMID 15447792 · PMC523852 · BMC medical genetics · 2004 · 8 claims · 8 setups

Full-text index only

TMPRSS3 mutations were identified in four additional Pakistani families with recessive, nonsyndromic congenital deafness co-segregating with DFNB8/B10 haplotypes

pakistani affected retina tissues linkage sanger race

Experiments

PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

Genetic Dissection of Tissue-Specific Apolipoprotein E Function for Hypercholesterolemia and Diet-Induced Obesity.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

GENCODE: producing a reference annotation for ENCODE.

Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.

Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

Candidate target genes for loss of heterozygosity on human chromosome 17q21.

GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology.

Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

Identification of novel homologous microRNA genes in the rhesus macaque genome.

Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.

Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene.

Estimation of genetic parameters and genome-wide association study for carcass traits in native chickens.

Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.