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 61

System / cell line: long ✕ Assay: genomic ✕ Clear

Eight previously unidentified mutations found in the OA1 ocular albinism gene.

PMID 16646960 · PMC1468396 · BMC medical genetics · 2006 · 7 claims · 5 setups

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Sequencing of the nine OA1 exons in 72 individuals identified ten different mutations across seven unrelated families and three sporadic cases.

genomic oa1 direct long-range splice-site
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
Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

PMID 41629338 · PMC12966425 · Scientific data · 2026 · 8 claims · 8 setups

Has reproduction · 91

A chromosome-level genome assembly of G. vermiculophylla was generated by combining DNBSeq short reads, Nanopore long reads, and Hi-C data.

gracilaria whole-genome nanopore hi-c
X-linked hyper IgM (HIGM1) in an African kindred: the first report from South Africa.

PMID 14641931 · PMC317313 · BMC pediatrics · 2003 · 7 claims · 5 setups

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This is the first fully characterized South African family with X-linked hyper-IgM syndrome (HIGM1)

activated pbmcs genomic pcr flow rt-pcr long-range
Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups

Has reproduction

Transposable elements make up nearly 45% of the human genome, vastly exceeding the ~1.5% that is protein-coding.

genome normal drosophila long short-read whole-genome synthetic
Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

PMID 19133980 · PMC4303606 · British journal of haematology · 2009 · 7 claims · 6 setups

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Downregulation of GR mRNA in the resistant myeloma cell line is caused by a block to transcriptional elongation within intron B of the GR gene

mm.1s pcr demethylating quantitative
Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

PMID 20011630 · PMC2790479 · Molecular vision · 2009 · 8 claims · 5 setups

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MDH1 is not the causative gene for RP28-linked autosomal recessive retinitis pigmentosa

genomic lr-pcr uhts v-4 long-range ultra sanger
Analysis of TSG101 tumour susceptibility gene transcripts in cervical and endometrial cancers.

PMID 10027311 · PMC2362423 · British journal of cancer · 1999 · 6 claims · 5 setups

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Abnormal (aberrant) TSG101 transcripts are common in both cancerous and non-cancerous cervical/endometrial tissue as well as in normal peripheral mononuclear cells

cervical peripheral rt-pcr southern long
Shotgun haplotyping: a novel method for surveying allelic sequence variation.

PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

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A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

genomic long pcr ampicillin-resistant long cloning short
Genomic characterization of five deletions in the LDL receptor gene in Danish Familial Hypercholesterolemic subjects.

PMID 16796766 · PMC1523332 · BMC medical genetics · 2006 · 7 claims · 5 setups

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All five LDLR deletions are flanked by Alu elements, supporting unequal homologous recombination between Alu repeats as the causative mechanism

genomic pcr-amplified ldlr blood long-range cycle diagnostic
Mutation spectrum of 122 hemophilia A families from Taiwanese population by LD-PCR, DHPLC, multiplex PCR and evaluating the clinical application of HRM.

PMID 18565236 · PMC2442058 · BMC medical genetics · 2008 · 7 claims · 6 setups

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The combined LD-PCR/DHPLC diagnostic strategy achieved a 100% mutation detection rate across 122 Taiwanese hemophilia A families.

genomic pcr long-distance pcr sanger
Genomic structure and alterations of homeobox gene CDX2 in colorectal carcinomas.

PMID 10027310 · PMC2362430 · British journal of cancer · 1999 · 8 claims · 6 setups

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CDX2 expression is decreased in colorectal carcinomas in prior studies

genomic sporadic hnpcc carcinoma standard pcr-sscp cloning
A chromosome-level genome assembly of Plantago ovata.

PMID 36707685 · PMC9883528 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 99

A chromosome-level reference genome assembly of P. ovata was constructed using PacBio long reads and Hi-C scaffolding.

plantago ovata pacbio hi-c k-mer
Detecting natural selection by empirical comparison to random regions of the genome.

PMID 19783549 · PMC2778377 · Human molecular genetics · 2009 · 8 claims · 5 setups

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Comparing candidate loci to empirically matched random genomic regions (ENCODE data) avoids the strong demographic/mutation assumptions required by theoretical neutral models and provides a robust test for selection

ceu genomic simulated long-read snp population
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

PMID 36262335 · PMC9557141 · F1000Research · 2022 · 7 claims · 3 setups

Has reproduction · 59

The third BCM & DNAnexus hackathon produced nine software projects for SV analysis, of which eight are presented in this paper.

long-read re-sequenced genomic long-read k-mer read-based
An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

PMID 18384666 · PMC2373789 · BMC genomics · 2008 · 8 claims · 7 setups

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The bovine genome contains a cluster of eight SERPINA3 genes and one pseudogene (SERPINA3P) sharing high sequence identity and identical structural organization

bovine bac roslin deduced southern bac radiation
Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer.

PMID 19644707 · PMC2778717 · Human genetics · 2009 · 7 claims · 5 setups

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Resequencing of the 97-kb 10q11.2 region identified 241 novel polymorphisms not previously reported in dbSNP

genomic plco hapmap computational targeted long-range genotype
Deletion of the V2 vasopressin receptor gene in two Chinese patients with nephrogenic diabetes insipidus.

PMID 17101063 · PMC1657029 · BMC genetics · 2006 · 7 claims · 6 setups

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The two NDI patients carry a 5,995-bp genomic deletion combined with a 3-bp (GAG) insertion at Xq28 that removes the entire AVPR2 gene and the last exon (exon 22) of the C1 (ARHGAP4) gene.

genomic proband blood patients pcr long-range combined
Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

genomic commercial plco unrelated targeted long-range genotyping
Search for genetic variants in the p66Shc longevity gene by PCR-single strand conformational polymorphism in patients with early-onset cardiovascular disease.

PMID 16519809 · PMC1420326 · BMC genetics · 2006 · 7 claims · 2 setups

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p66Shc gene increases intracellular reactive oxygen species (ROS), affecting the rate of oxidative damage to nucleic acids

genomic pcr-single direct

Experiments

Eight previously unidentified mutations found in the OA1 ocular albinism gene.

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

Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

X-linked hyper IgM (HIGM1) in an African kindred: the first report from South Africa.

Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

Analysis of TSG101 tumour susceptibility gene transcripts in cervical and endometrial cancers.

Shotgun haplotyping: a novel method for surveying allelic sequence variation.

Genomic characterization of five deletions in the LDL receptor gene in Danish Familial Hypercholesterolemic subjects.

Mutation spectrum of 122 hemophilia A families from Taiwanese population by LD-PCR, DHPLC, multiplex PCR and evaluating the clinical application of HRM.

Genomic structure and alterations of homeobox gene CDX2 in colorectal carcinomas.

A chromosome-level genome assembly of Plantago ovata.

Detecting natural selection by empirical comparison to random regions of the genome.

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer.

Deletion of the V2 vasopressin receptor gene in two Chinese patients with nephrogenic diabetes insipidus.

Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

Search for genetic variants in the p66Shc longevity gene by PCR-single strand conformational polymorphism in patients with early-onset cardiovascular disease.