A novel RNA sequencing data analysis method for cell line authentication (Q31161522)

21 August 2017

A novel RNA sequencing data analysis method for cell line authentication (English)

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Cristina Al-Khalili Szigyarto

21 August 2017

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7

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8

object named as

Cristina Al-Khalili Szigyarto

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Susan Kennedy

object named as

Susan Kennedy

3

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Erik Fasterius

object named as

Erik Fasterius

1

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author name string

Cinzia Raso

2

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21 August 2017

Nora Rauch

4

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21 August 2017

Pär Lundin

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21 August 2017

Walter Kolch

6

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21 August 2017

language of work or name

English

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publication date

13 February 2017

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21 August 2017

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21 August 2017

12

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21 August 2017

e0171435

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21 August 2017

2

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Creative Commons Attribution 4.0 International

21 August 2017

start time

13 February 2017

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

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DESeq2

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CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Authentication: A Standard Problem or a Problem of Standards?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Standards for Cell Line Authentication and Beyond

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

CCAT1 is an enhancer-templated RNA that predicts BET sensitivity in colorectal cancer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Systematic comparison of variant calling pipelines using gold standard personal exome variants

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Reproducibility: changing the policies and culture of cell line authentication

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

A resource for cell line authentication, annotation and quality control

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Human biosample authentication using the high-throughput, cost-effective SNPtrace(TM) system

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Comprehensive high-throughput RNA sequencing analysis reveals contamination of multiple nasopharyngeal carcinoma cell lines with HeLa cell genomes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

On-beads digestion in conjunction with data-dependent mass spectrometry: a shortcut to quantitative and dynamic interaction proteomics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

U-251 revisited: genetic drift and phenotypic consequences of long-term cultures of glioblastoma cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Reliable identification of genomic variants from RNA-seq data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

STAR: ultrafast universal RNA-seq aligner

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Recommendation of short tandem repeat profiling for authenticating human cell lines, stem cells, and tissues

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Check your cultures! A list of cross-contaminated or misidentified cell lines

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Mapping and quantifying mammalian transcriptomes by RNA-Seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Database resources of the National Center for Biotechnology Information

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Species identification in cell culture: a two-pronged molecular approach

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Did the four human cancer cell lines DLD-1, HCT-15, HCT-8, and HRT-18 originate from one and the same patient?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Altered growth of human colon cancer cell lines disrupted at activated Ki-ras

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

DLD-1 and HCT-15 cell lines derived separately from colorectal carcinomas have totally different chromosome changes but the same genetic origin

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Heterogeneity of malignant cells from a human colonic carcinoma.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Determination of the levels of urokinase and its receptor in human colon carcinoma cell lines

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Proliferation of the human colon carcinoma cell line HT29: autocrine growth and deregulated expression of the c-myc oncogene

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Tumor and lymphoid cell lines from a patient with carcinoma of the colon for a cytotoxicity model

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Chemotherapy of cell-line-derived human colon carcinomas in mice immunosuppressed with antithymocyte serum

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5305277

Erratum: Near-optimal probabilistic RNA-seq quantification

14 July 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28192450

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Cell line misidentification: the beginning of the end

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28192450

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0171435

1 reference

21 August 2017

0 references

1 reference

21 August 2017

1 reference