ArticlePloS one2017
A novel RNA sequencing data analysis method for cell line authentication.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 30 citations in OpenAlex.
- RNA-seq-derived sequence variations are excellent features for cell line identification.Computational and structural biotechnology journal · 2025Article
- GenoPipe: identifying the genotype of origin within (epi)genomic datasets.Nucleic acids research · 2023Article
- CCLHunter: An efficient toolkit for cancer cell line authentication.Computational and structural biotechnology journal · 2023Article
- Effect ofFrontiers in cell and developmental biology · 2022Article
- Review
- Approaching RNA-seq for Cell Line Identification.Bio-protocol · 2020Article
- Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASNature communications · 2020Article
- Single-cell RNA-seq variant analysis for exploration of genetic heterogeneity in cancer.Scientific reports · 2019Article
- Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASBritish journal of cancer · 2019Article
- Multi-omic measurements of heterogeneity in HeLa cells across laboratories.Nature biotechnology · 2019Article
- PDEδ inhibition impedes the proliferation and survival of human colorectal cancer cell lines harboring oncogenic KRas.International journal of cancer · 2019Article
- Subverted regulation of Nox1 NADPH oxidase-dependent oxidant generation by protein disulfide isomerase A1 in colon carcinoma cells with overactivated KRas.Cell death & disease · 2019Article
- CeL-ID: cell line identification using RNA-seq data.BMC genomics · 2019Article
- Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations.Scientific reports · 2018Article
- Oncogenic KRAS suppresses store-operated CaCell calcium · 2018Article
- Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.Oncotarget · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. Using both public and novel data, we demonstrate the use of RNA-sequencing data analysis for cell line authentication by examining the validity of COLO205, DLD1, HCT15, HCT116, HKE3, HT29 and RKO colorectal cancer cell lines. We successfully authenticate the studied cell lines and validate previous reports indicating that DLD1 and HCT15 are synonymous. We also show that the analysed HKE3 cells harbour an unexpected KRAS-G13D mutation and confirm that this cell line is a genuine KRAS dosage mutant, rather than a true isogenic derivative of HCT116 expressing only the wild type KRAS. This authentication method could be used to revisit the numerous cell line based RNA sequencing experiments available in public data repositories, analyse new experiments where whole genome sequencing is not available, as well as facilitate comparisons of data from different experiments, platforms and laboratories.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.