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 70

System / cell line: lines ✕ Assay: allele ✕ Clear

Allele quantification using molecular inversion probes (MIP).

PMID 16314297 · PMC1301601 · Nucleic acids research · 2005 · 8 claims · 5 setups

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MIP technology at high multiplex (>20,000 SNPs) can provide copy number measurements while simultaneously obtaining allele information

reference ffpe lines na18573 mip restriction quantitative
Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

PMID 19116668 · PMC2605564 · PloS one · 2008 · 7 claims · 6 setups

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ASE is more robust than total gene expression approaches to environmental variation and trans-acting genetic factors, giving a cleaner representation of cis-acting effects.

hapmap combined coriell ceu allele-specific linear one-sample
Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

PMID 17608949 · PMC1934372 · BMC genomics · 2007 · 7 claims · 5 setups

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Developed a statistical model-fitting method to infer generalized (multi-allelic, copy-number-aware) genotypes from raw SNP microarray data

individuals mother-father-child transcribed snp quantitative multiplex
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

PMID 19808877 · PMC2788925 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 6 setups

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Reads mapped to the reference genome show a significant bias toward the reference allele at heterozygous SNPs

lymphoblastoid simulated hapmap genes rna-seq read-mapping eqtl
Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.

PMID 36869353 · PMC9983196 · Genome biology · 2023 · 8 claims · 5 setups

Has reproduction · 64

HiCFlow, a new bioinformatic pipeline, performs de novo haplotype assembly, phasing, and visualization of allele-specific (parental) chromatin conformation directly from Hi-C data without requiring pre-phased haplotypes.

1-7hb2 gm12878 imr-90 lines region hi-c genome-wide
Detecting imbalanced expression of SNP alleles by minisequencing on microarrays.

PMID 15500681 · PMC529269 · BMC biotechnology · 2004 · 8 claims · 7 setups

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Both microarray minisequencing formats accurately quantify SNP allele ratios, with R2 > 0.95 for the majority of regression lines

genomic huvec microarray solid-phase real-time
The detection of K-ras mutations in colorectal cancer using the amplification-refractory mutation system.

PMID 9579832 · PMC2150152 · British journal of cancer · 1998 · 5 claims · 6 setups

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ARMS reliably detects K-ras codon 12/13 mutations in archival CRC DNA samples even when mutant sequence is under-represented relative to wild-type

archival tumour tumour-derived haematoxylin arms direct pcr
An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

PMID 19838300 · PMC2759515 · PloS one · 2009 · 8 claims · 7 setups

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An nc-rRNA is transcribed from the intergenic spacer upstream of the rRNA transcription start site in human lung epithelial and lung cancer cells, spanning roughly -1000 to at least +203/+300.

lung hpl1d rrna external pcr rt-pcr quantitative
Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

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Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

tumors cancer tumor lung direct database quantitative
In vivo prime editing rescues alternating hemiplegia of childhood in mice.

PMID 40695277 · PMC12702498 · Cell · 2025 · 8 claims · 8 setups

Has reproduction · 84

PE and BE strategies efficiently correct five prevalent ATP1A3 mutations (D801N, E815K, L839P, G947R-A, G947R-C) in HEK293T cells and AHC patient-derived iPSCs, with 43%-90% correction in iPSCs.

hek293t ahc n2a b6c3.atp1a3 prime circle-seq rhampseq
Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.

PMID 36864379 · PMC9979506 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

Has reproduction · 100

French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population.

boars lwd lws pig whole-genome genetic genome-wide
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
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
Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

PMID 17267408 · PMC1865061 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Measuring allelic imbalance (AI) of two SNP alleles within the same sample is an effective approach for identifying cis-acting rSNPs, since each allele serves as an internal control for the other.

tumor promoter hela cdna bead tag-microarray
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

PMID 18418848 · PMC6668724 · Genes, chromosomes & cancer · 2008 · 6 claims · 5 setups

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Emulsion PCR combined with picotiter plate pyrosequencing (454 sequencing) enables high-resolution, high-throughput detection of low-frequency sequence variants among the many individual copies of an amplified gene.

erbb2-amplified erbb2-positive plasmid cos-7 emulsion serial immune-complex
Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

PMID 19811662 · PMC2766370 · Molecular cancer · 2009 · 7 claims · 6 setups

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LCN-HRM enables detection and sequencing-based characterisation of low-level mutations that are undetectable by direct sequencing alone

hct116 ffpe genomic tx84 dideoxynucleotide high lcn-hrm
High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: four cases of homozygous deletions of the CDKN2A gene.

PMID 18664255 · PMC2527340 · BMC genomics · 2008 · 8 claims · 3 setups

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Affymetrix 50K/250K SNP arrays with CNAG3.0 software provide high-resolution (10-12kb) copy number and allele-specific information suitable for characterizing chromosomal rearrangements in neuroblastoma tumors

neuroblastoma snp multiplex
Rare-type mutations of MMAC1 tumor suppressor gene in human glioma cell lines and their tumors of origin.

PMID 10551321 · PMC5926156 · Japanese journal of cancer research : Gann · 1999 · 8 claims · 6 setups

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6 of 10 glioma cell lines examined showed MMAC1 mutations with presumed loss of heterozygosity (LOH)

glioma pcr northern rt-pcr sscp
Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.

PMID 11985785 · PMC5927014 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 4 setups

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DHL-9 lymphoma cells lack detectable MTAP enzyme activity despite possessing an intact (non-deleted) MTAP gene

dhl-9 genomic lymphoblastoid hela pcr allele-specific luciferase

Experiments

Allele quantification using molecular inversion probes (MIP).

Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.

Detecting imbalanced expression of SNP alleles by minisequencing on microarrays.

The detection of K-ras mutations in colorectal cancer using the amplification-refractory mutation system.

An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

In vivo prime editing rescues alternating hemiplegia of childhood in mice.

Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.

Identification of common genetic variation that modulates alternative splicing.

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

Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

Genome-wide survey of allele-specific splicing in humans.

Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: four cases of homozygous deletions of the CDKN2A gene.

Rare-type mutations of MMAC1 tumor suppressor gene in human glioma cell lines and their tumors of origin.

Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.