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 49

System / cell line: cell-line ✕ Assay: copy ✕ Clear

SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

PMID 17192189 · PMC1764892 · BMC genomics · 2006 · 7 claims · 6 setups

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SIGMA is a user-friendly, web-based Java application for visualization and integrative analysis of array CGH data across multiple platforms.

cancer lung breast array medip segmentation
Integration of cytogenetic landmarks into the draft sequence of the human genome.

PMID 11237021 · PMC7845515 · Nature · 2001 · 8 claims · 6 setups

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7,600 cytogenetically defined landmarks (from a set of 8,877 clones) were placed on the draft sequence of the human genome as a public resource

large-insert bac ml-2 dgap012 fluorescence sts array
Human and mouse oligonucleotide-based array CGH.

PMID 16361265 · PMC1316119 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Oligo array CGH detects single copy gains, multi-copy amplifications, and homozygous/heterozygous deletions as small as 100 kb

bt474 normal gm01750 mda-mb-468 array fish
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
High resolution array-CGH analysis of single cells.

PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups

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Single copy number changes as small as 8.3 Mb can be detected reliably in single cells using GenomePlex WGA combined with high-resolution tiling-path array-CGH.

769p hct116 peripheral single array-cgh gel fish
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
Global variation in copy number in the human genome.

PMID 17122850 · PMC2669898 · Nature · 2006 · 8 claims · 6 setups

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A first-generation CNV map of the human genome was constructed from 270 HapMap individuals across four populations, identifying 1,447 CNV regions covering ~360 Mb (12%) of the genome.

hapmap subset blood snp array karyotyping
Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.

PMID 16420694 · PMC1382255 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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SNPscan is a web-accessible tool that displays SNP copy number, genotype call, and LOH p-value data together in a single plot per sample

lymphoblastoid skin ceph genomic snp array pcr
Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

PMID 17470268 · PMC1868757 · BMC genomics · 2007 · 8 claims · 7 setups

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graCNV uses re-annotated Affymetrix expression microarray probe sets and the WPP algorithm to measure DNA copy number variation at a median resolution of ~17,500 bp without genomic complexity reduction.

neuroblastoma same normal megabladder acgh bac principal
A statistical change point model approach for the detection of DNA copy number variations in array CGH data.

PMID 19875853 · PMC4154476 · IEEE/ACM transactions on computational biology and bioinformatics · 2009 · 7 claims · 4 setups

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A novel mean and variance change point model (MVCM) is proposed to detect CNVs/breakpoints in aCGH data.

simulated fibroblast breast simulation array
SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

single hcc2218 nsclc array gene multi-omics
SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

PMID 17971856 · PMC2034603 · PloS one · 2007 · 8 claims · 3 setups

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SiDCoN is a spreadsheet-based application that simulates Ballele and logR plots for all known types of DNA copy number change, with or without stromal contamination, for up to 5000 SNP data points and up to 3 combined aberrations

sidcon real mixtures snp re-analysis
Probing the cancer genome.

PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

mcf-7 tumor lung oral sanger solexa gistic
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
CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

PMID 16504045 · PMC1402331 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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CARAT is a novel algorithm that uses SNP probe intensity and genotype-based allelic dosage response in a regression framework to estimate allele-specific copy number genome-wide.

normal genomic sk-br-3 cancer snp quantitative allele-specific
Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

PMID 19706770 · PMC2745517 · Cancer research · 2009 · 8 claims · 8 setups

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Genome-wide DNA copy number analysis of 161 primary breast tumors identified six novel focally amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4

breast mcf10a mcf10ca1h snp quantitative rt-qpcr
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.

PMID 38781959 · PMC11228554 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

Has reproduction · 76

DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs across patients and samples

fresh matched archived dsrct scrna-seq single-nucleus bulk
Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow.

PMID 18074030 · PMC2111048 · PloS one · 2007 · 8 claims · 7 setups

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MDA-based single-cell whole-genome amplification (S-WGA) products show large variability in amplification bias, including allele dropout and preferential amplification.

lymphoblastoid lcl cmk11-5 gel taqman oligonucleotide
Statistical framework for calling allelic imbalance in high-throughput sequencing data.

PMID 39966391 · PMC11836314 · Nature communications · 2025 · 8 claims · 6 setups

Has reproduction · 89

MIXALIME is a versatile computational framework for calling allele-specific variants (ASVs) from diverse high-throughput omics data

wa01 left heart chip-seq rna-seq cage-seq
Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.

PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups

Has reproduction · 71

DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue

ucec ishikawa rna-seq proteomics immunohistochemistry

Experiments

SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

Integration of cytogenetic landmarks into the draft sequence of the human genome.

Human and mouse oligonucleotide-based array CGH.

Allele quantification using molecular inversion probes (MIP).

High resolution array-CGH analysis of single cells.

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

Global variation in copy number in the human genome.

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

A statistical change point model approach for the detection of DNA copy number variations in array CGH data.

SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

Probing the cancer genome.

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

CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.

Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow.

Statistical framework for calling allelic imbalance in high-throughput sequencing data.

Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.