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 362

System / cell line: cdna ✕ Clear

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
ECgene: genome annotation for alternative splicing.

PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

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ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

brca2 rgs17 organs cdna genomic genome transcript
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

lncap lncap-derived r1881-treated massively blast blat
Is a genetic defect in Fkbp6 a common cause of azoospermia in humans?

PMID 16983454 · PMC6275806 · Cellular & molecular biology letters · 2006 · 7 claims · 7 setups

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Human FKBP6 expression is restricted to the testis among 15 adult tissues examined

genomic bilateral testicular rt-pcr mutation testicular
Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays.

PMID 17430969 · PMC1888820 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Developed an LPE-based error-pooling and weighted ANOVA modeling approach for statistical analysis of high-density tiling array data

cell-cycle-synchronized hela computational differentially tiling cdna statistical
Mutations in the focal adhesion targeting region of deleted in liver cancer-1 attenuate their expression and function.

PMID 18829524 · PMC2597479 · Cancer research · 2008 · 8 claims · 6 setups

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The DLC-1 fragment spanning residues 201-500 is sufficient for focal adhesion targeting (FAT region)

a549 prostate colon mda-mb-468 immunofluorescence pcr colony
RPS4Y gene family evolution in primates.

PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

primate chromosomes rps4x concatenated pcr fluorescence repeat
Next-generation high-density self-assembling functional protein arrays.

PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups

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A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success

test high-density amine-coated array picogreen anti-gst fluorescently
DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

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DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

normal dld1 beas2b ramos tss comparative
Gene Ontology annotations: what they mean and where they come from.

PMID 18460184 · PMC2367625 · BMC bioinformatics · 2008 · 7 claims · 3 setups

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A GO annotation is a formal statement linking a gene product type to a molecular function, biological process, or cellular component type, based on experimental observations or inferences.

extract embryo preimplantation enzymatic mutational immunofluorescence
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups

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Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.

genomic cdna known sequence homology transcript
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 90

Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)

vero calu-3 genes direct pcr poly
Distinct mutations in two patients with leukocyte adhesion deficiency and their functional correlates.

PMID 1694220 · PMC2188166 · The Journal of experimental medicine · 1990 · 8 claims · 8 setups

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Patient 14 (moderate phenotype) carries a C-to-T substitution at nucleotide 517 of the beta subunit cDNA, changing amino acid 149 from leucine to proline

ebv-transformed cos 51cr-labeled rnase cdna pcr
Characterization of in vivo somatic mutations at the hypoxanthine phosphoribosyltransferase gene of a human control population.

PMID 8513767 · PMC1519656 · Environmental health perspectives · 1993 · 7 claims · 4 setups

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In vivo hprt mutants from 63 independent donors were molecularly characterized by cDNA and genomic DNA PCR/sequencing.

peripheral hprt-mutant pcr limiting cdna multiplex
The gene guessing game.

PMID 11025532 · PMC2448377 · Yeast (Chichester, England) · 2000 · 8 claims · 6 setups

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Published methods for estimating human gene number diverge widely, from ~30,000 to over 140,000 genes.

genomic ests tetraodon genome cpg est comparative
Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

PMID 16195578 · PMC1240112 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Alternative splices in 10,818 human-mouse gene pairs can be classified as conserved, novel, or diverged based on genomic and transcript-level cross-species comparison.

orthologous diverse tissues gene comparative est microarray
Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments.

PMID 15860768 · PMC1087789 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Selector oligonucleotides can circularize many distinct genomic restriction fragments in one reaction, enabling parallel amplification with a single universal primer pair instead of multiple target-specific primer pairs

genomic 7776-clone selector-based cdna restriction
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
Evolutionarily conserved human targets of adenosine to inosine RNA editing.

PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

panel brain chicken flna comparative rt-pcr homology
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

Has reproduction · 27

A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

radish assembled rna-seq novo functional

Experiments

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

ECgene: genome annotation for alternative splicing.

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

Is a genetic defect in Fkbp6 a common cause of azoospermia in humans?

Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays.

Mutations in the focal adhesion targeting region of deleted in liver cancer-1 attenuate their expression and function.

RPS4Y gene family evolution in primates.

Next-generation high-density self-assembling functional protein arrays.

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

Gene Ontology annotations: what they mean and where they come from.

SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

Distinct mutations in two patients with leukocyte adhesion deficiency and their functional correlates.

Characterization of in vivo somatic mutations at the hypoxanthine phosphoribosyltransferase gene of a human control population.

The gene guessing game.

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments.

Speeding disease gene discovery by sequence based candidate prioritization.

Evolutionarily conserved human targets of adenosine to inosine RNA editing.

Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.