Small RNA profiling of low biomass samples: identification and removal of contaminants

Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne; Etheridge, Alton; Fritz, Joelle V.; May, Patrick; de Beaufort, Carine; Upadhyaya, Bimal B.; Ghosal, Anubrata; Galas, David J.; Wilmes, Paul

doi:10.1186/s12915-018-0522-7

Title: Small RNA profiling of low biomass samples: identification and removal of contaminants

Journal Article · Mon May 14 00:00:00 EDT 2018 · BMC Biology

DOI:https://doi.org/10.1186/s12915-018-0522-7· OSTI ID:1441216

Heintz-Buschart, Anna ^[1]; Yusuf, Dilmurat ^[2]; Kaysen, Anne ^[3]; Etheridge, Alton ^[4]; Fritz, Joelle V. ^[3]; May, Patrick ^[5]; de Beaufort, Carine ^[3]; Upadhyaya, Bimal B. ^[5]; Ghosal, Anubrata ^[6]; Galas, David J. ^[4];

^[5]

Univ. of Luxembourg, Esch-sur-Alzette (Luxembourg); German Centre for Integrative Biodiversity Research (iDiv) Leipzig-Halle-Jena, Leipzig (Germany); Helmholtz-Centre for Environmental Research GmbH (UFZ), Halle (Germany)
Univ. of Luxembourg, Esch-sur-Alzette (Luxembourg); Univ. of Freiburg, Freiburg (Germany)
Univ. of Luxembourg, Esch-sur-Alzette (Luxembourg); Centre Hospitalier de Luxembourg, Luxembourg (Luxembourg)
Pacific Northwest Research Institute, Seattle, WA (United States)
Univ. of Luxembourg, Esch-sur-Alzette (Luxembourg)
Univ. of Luxembourg, Esch-sur-Alzette (Luxembourg); Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

Here, sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. DNA contamination has been previously reported, yet contamination with RNA is usually considered to be very unlikely due to its inherent instability. Small RNAs (sRNAs) identified in tissues and bodily fluids, such as blood plasma, have implications for physiology and pathology, and therefore the potential to act as disease biomarkers. Thus, the possibility for RNA contaminants demands careful evaluation.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-76RL01830; ATTRACT/A09/03; CORE/15/BM/10404093; CORE/16/BM/11276306; PoC/13/02; 1180851; 5821107; CORE14/BM/8066232; 1U01HL126496; ImMicroDyn1

OSTI ID:: 1441216

Journal Information:: BMC Biology, Vol. 16, Issue 1; ISSN 1741-7007

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 34 works

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The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions

Journal Article · Thu Aug 30 00:00:00 EDT 2018 · Frontiers in Microbiology · OSTI ID:1441216

Malabirade, Antoine; Habier, Janine; Heintz-Buschart, Anna; +7 more

Detection of mycobacterial small RNA in the bacterial culture supernatant and plasma of patients with active tuberculosis

Journal Article · Sat Sep 15 00:00:00 EDT 2018 · Biochemical and Biophysical Research Communications · OSTI ID:1441216

Fu, Yingmei; Li, Wenjing; Wu, Zheng; +3 more

Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

Technical Report · Mon May 17 00:00:00 EDT 2010 · OSTI ID:1441216

Burns, Andrew; Joachimiak, Marcin; Deutschbauer, Adam; +2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
RNA sequencing
Artefact removal
Exogenous RNA in human blood plasma
Contaminant RNA
Spin columns

Contaminomics Heintz-Buschart, Anna; May, Patrick https://doi.org/10.5281/ZENODO.1209974 The current record is supplemented by this software	software	March 2018
Additional file1: of Small RNA profiling of low biomass samples: identification and removal of contaminants Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.6268769 The current record is supplemented by this dataset	dataset	May 2018
Additional file1: of Small RNA profiling of low biomass samples: identification and removal of contaminants Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.6268769.v1 The current record is supplemented by this dataset	dataset	May 2018
Additional file 2: of Small RNA profiling of low biomass samples: identification and removal of contaminants Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/M9.FIGSHARE.6268790 The current record is supplemented by this dataset	dataset	May 2018
Additional file 2: of Small RNA profiling of low biomass samples: identification and removal of contaminants Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.6268790.v1 The current record is supplemented by this dataset	dataset	May 2018
Additional file 3: of Small RNA profiling of low biomass samples: identification and removal of contaminants Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.6268817 The current record is supplemented by this dataset	dataset	May 2018
Additional file 3: of Small RNA profiling of low biomass samples: identification and removal of contaminants Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.6268817.v1 The current record is supplemented by this figure	figure	May 2018
Additional file 4: of Small RNA profiling of low biomass samples: identification and removal of contaminants Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.6268832 The current record is supplemented by this figure	figure	May 2018
Additional file 4: of Small RNA profiling of low biomass samples: identification and removal of contaminants Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.6268832.v1 The current record is supplemented by this dataset	dataset	May 2018
Additional file 5: of Small RNA profiling of low biomass samples: identification and removal of contaminants Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.6268841 The current record is supplemented by this dataset	dataset	May 2018
Additional file 5: of Small RNA profiling of low biomass samples: identification and removal of contaminants Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.6268841.v1 The current record is supplemented by this figure	figure	May 2018
Small RNA profiling of low biomass samples: identification and removal of contaminants [Supplementary Data] Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.c.4100117 The current record is supplemented by this collection	collection	May 2018
Small RNA profiling of low biomass samples: identification and removal of contaminants [Supplementary Data] Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne https://doi.org/10.6084/m9.figshare.c.4100117.v1 The current record is supplemented by this dataset	dataset	May 2018