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 21

System / cell line: transcripts ✕ Assay: sanger ✕ Clear

Somatic and germline mutation in GRIM-19, a dual function gene involved in mitochondrial metabolism and cell death, is linked to mitochondrion-rich (Hurthle cell) tumours of the thyroid.

PMID 15841082 · PMC2361763 · British journal of cancer · 2005 · 8 claims · 5 setups

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Somatic missense GRIM-19 mutations occur in a subset of sporadic Hürthle cell carcinomas but not in non-Hürthle cell thyroid carcinomas or blood donors

sporadic hürthle pcr loss semi-quantitative
Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families.

PMID 17010193 · PMC1599749 · BMC cancer · 2006 · 8 claims · 4 setups

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No germline deleterious mutations were identified in the ATR coding region among 54 non-BRCA1/2 high-risk French Canadian breast cancer cases.

genomic ebv-transformed normal direct linkage rt-pcr
Identification of the first intragenic deletion of the PITX2 gene causing an Axenfeld-Rieger Syndrome: case report.

PMID 17134502 · PMC1684248 · BMC medical genetics · 2006 · 8 claims · 8 setups

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An intragenic deletion of 3,059 bp within the PITX2 gene, spanning the end of exon 5 through the start of exon 6, causes this family's severe ARS phenotype

genomic lymphoblastoid i-2 patients pcr quantitative long-range
Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based
Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
ChimerDB 2.0--a knowledgebase for fusion genes updated.

PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

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ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

genbank sra pubmed transcript-to-genome ngs literature
Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2.

PMID 19744353 · PMC2749023 · BMC medical genetics · 2009 · 8 claims · 6 setups

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Gross mutations (exon deletions and intragenic insertions) are a frequent, not rare, cause of AOA2

genomic peripheral setx sanger dosage long-range
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 38

A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

gossypium uppermost root reads bulk leaf rt-qpcr
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

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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
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

PMID 19835606 · PMC2784330 · Genome biology · 2009 · 7 claims · 2 setups

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Hybrid selection of cDNA dramatically increases the specificity of sequencing reads mapping to targeted cancer-related transcripts.

k-562 targeted sanger
Genes on bovine chromosome 18 associated with bilateral convergent strabismus with exophthalmos in German Brown cattle.

PMID 18836565 · PMC2556974 · Molecular vision · 2008 · 8 claims · 5 setups

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Haplotype association analysis refines the BCSE-linked region on BTA18 to a 6.82 Mb interval spanning 56.05–62.87 Mb

eye genomic tnnt1 cdna genomic snp
Ensembl 2006.

PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

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Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

cow ensembl snps genome gene whole-genome pairwise
Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

PMID 16840528 · PMC1524903 · Nucleic acids research · 2006 · 7 claims · 5 setups

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MS-PET, which dimerizes PETs prior to 454 multiplex sequencing, achieves an approximate 100-fold efficiency increase over standard Sanger-based PET analysis

mcf7 hct116 flcdna gis-pet chip-pet quantitative
ChimerDB--a knowledgebase for fusion sequences.

PMID 16381848 · PMC1347382 · Nucleic acids research · 2006 · 8 claims · 6 setups

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ChimerDB integrates bioinformatics analysis of mRNA/EST sequences, manually collected literature data, and OMIM translocation data into a single fusion sequence knowledgebase

genome candidate pubmed omim blat splice-site ecgene
Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer.

PMID 18489799 · PMC2413254 · BMC cancer · 2008 · 8 claims · 6 setups

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Pathogenic BRCA1/BRCA2 mutations were identified in 294 of 1,010 (29.1%) unrelated high-risk Czech probands

genomic pcr-amplified brca1 pha-stimulated truncation heteroduplex direct
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

PMID 18438408 · PMC2705838 · Nature genetics · 2008 · 8 claims · 8 setups

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Massively parallel paired-end sequencing can characterize somatic and germline structural rearrangements to base-pair resolution across a whole cancer genome

nci-h2171 nci-h1770 massively genomic rt-pcr
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

Has reproduction · 50

330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

brassica r500 rapa genomic bulk reference-based snp
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

Has reproduction · 57

ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

arabidopsis pacbio randomly illumina pacbio nanopore
Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

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A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

cdna image hbs1l ahi1 rt-pcr est northern
Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

bovine pcr-based comparative rt-pcr

Experiments

Somatic and germline mutation in GRIM-19, a dual function gene involved in mitochondrial metabolism and cell death, is linked to mitochondrion-rich (Hurthle cell) tumours of the thyroid.

Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families.

Identification of the first intragenic deletion of the PITX2 gene causing an Axenfeld-Rieger Syndrome: case report.

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

ChimerDB 2.0--a knowledgebase for fusion genes updated.

Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2.

RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

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

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

Genes on bovine chromosome 18 associated with bilateral convergent strabismus with exophthalmos in German Brown cattle.

Ensembl 2006.

Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

ChimerDB--a knowledgebase for fusion sequences.

Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer.

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.