Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood
<p dir="ltr">Transcriptome profiling of human whole blood is used to discover biomarkers of diseases and to assess phenotypic traits. Recently, finger-stick blood collection systems have allowed a less invasive and quicker collection of peripheral blood. Such non-invasive sampling of...
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| مؤلفون آخرون: | , , , , , , , , , |
| منشور في: |
2023
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| _version_ | 1864513528349589504 |
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| author | Mahesh Kumar Reddy Kalikiri (17886695) |
| author2 | Harshitha Shobha Manjunath (14166132) Fazulur Rehaman Vempalli (14778577) Lisa Sara Mathew (17886698) Li Liu (75607) Li Wang (15202) Guishuang Wang (17886701) Kun Wang (134525) Oleksandr Soloviov (17886704) Stephan Lorenz (466378) Sara Tomei (3441323) |
| author2_role | author author author author author author author author author author |
| author_facet | Mahesh Kumar Reddy Kalikiri (17886695) Harshitha Shobha Manjunath (14166132) Fazulur Rehaman Vempalli (14778577) Lisa Sara Mathew (17886698) Li Liu (75607) Li Wang (15202) Guishuang Wang (17886701) Kun Wang (134525) Oleksandr Soloviov (17886704) Stephan Lorenz (466378) Sara Tomei (3441323) |
| author_role | author |
| dc.creator.none.fl_str_mv | Mahesh Kumar Reddy Kalikiri (17886695) Harshitha Shobha Manjunath (14166132) Fazulur Rehaman Vempalli (14778577) Lisa Sara Mathew (17886698) Li Liu (75607) Li Wang (15202) Guishuang Wang (17886701) Kun Wang (134525) Oleksandr Soloviov (17886704) Stephan Lorenz (466378) Sara Tomei (3441323) |
| dc.date.none.fl_str_mv | 2023-03-03T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1038/s41598-023-30629-5 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Technical_assessment_of_different_extraction_methods_and_transcriptome_profiling_of_RNA_isolated_from_small_volumes_of_blood/25125599 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Biochemistry and cell biology Bioinformatics and computational biology Genetics Transcriptome profiling Biomarkers Finger-stick blood collection systems Non-invasive sampling Blood extraction methods RNA isolation Tempus Spin RNA Isolation kit Transcriptomic data Illumina NextSeq 500 system Gene expression data RNA Gene expression profiling RNA integrity number (RIN) RNA-seq data analysis |
| dc.title.none.fl_str_mv | Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">Transcriptome profiling of human whole blood is used to discover biomarkers of diseases and to assess phenotypic traits. Recently, finger-stick blood collection systems have allowed a less invasive and quicker collection of peripheral blood. Such non-invasive sampling of small volumes of blood offers practical advantages. The quality of gene expression data is strictly dependent on the steps used for the sample collection, extraction, preparation and sequencing. Here we have: (i) compared the manual and automated RNA extraction of small volumes of blood using the Tempus Spin RNA isolation kit and the MagMAX for Stabilized Blood RNA Isolation kit , respectively; and (ii) assessed the effect of TURBO DNA Free treatment on the transcriptomic data of RNA isolated from small volumes of blood. We have used the QuantSeq 3′ FWD mRNA-Seq Library Prep kit to prepare RNA-seq libraries, which were sequenced on the Illumina NextSeq 500 system. The samples isolated manually displayed a higher variability in the transcriptomic data as compared to the other samples. The TURBO DNA Free treatment affected the RNA samples negatively, decreasing the RNA yield and reducing the quality and reproducibility of the transcriptomic data. We conclude that automated extraction systems should be preferred over manual extraction systems for data consistency, and that the TURBO DNA Free treatment should be avoided when working on RNA samples isolated manually from small volumes of blood.</p><h2>Other Information</h2><p dir="ltr">Published in: Scientific Reports<br>License: <a href="https://creativecommons.org/licenses/by/4.0" target="_blank">https://creativecommons.org/licenses/by/4.0</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1038/s41598-023-30629-5" target="_blank">https://dx.doi.org/10.1038/s41598-023-30629-5</a></p><p dir="ltr">Additional institutions affiliated with: Integrated Genomics Services - Sidra Medicine</p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_b420205985f90e7b994bb73b5905bf04 |
| identifier_str_mv | 10.1038/s41598-023-30629-5 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/25125599 |
| publishDate | 2023 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of bloodMahesh Kumar Reddy Kalikiri (17886695)Harshitha Shobha Manjunath (14166132)Fazulur Rehaman Vempalli (14778577)Lisa Sara Mathew (17886698)Li Liu (75607)Li Wang (15202)Guishuang Wang (17886701)Kun Wang (134525)Oleksandr Soloviov (17886704)Stephan Lorenz (466378)Sara Tomei (3441323)Biological sciencesBiochemistry and cell biologyBioinformatics and computational biologyGeneticsTranscriptome profilingBiomarkersFinger-stick blood collection systemsNon-invasive samplingBlood extraction methodsRNA isolationTempus Spin RNA Isolation kitTranscriptomic dataIllumina NextSeq 500 systemGene expression dataRNAGene expression profilingRNA integrity number (RIN)RNA-seq data analysis<p dir="ltr">Transcriptome profiling of human whole blood is used to discover biomarkers of diseases and to assess phenotypic traits. Recently, finger-stick blood collection systems have allowed a less invasive and quicker collection of peripheral blood. Such non-invasive sampling of small volumes of blood offers practical advantages. The quality of gene expression data is strictly dependent on the steps used for the sample collection, extraction, preparation and sequencing. Here we have: (i) compared the manual and automated RNA extraction of small volumes of blood using the Tempus Spin RNA isolation kit and the MagMAX for Stabilized Blood RNA Isolation kit , respectively; and (ii) assessed the effect of TURBO DNA Free treatment on the transcriptomic data of RNA isolated from small volumes of blood. We have used the QuantSeq 3′ FWD mRNA-Seq Library Prep kit to prepare RNA-seq libraries, which were sequenced on the Illumina NextSeq 500 system. The samples isolated manually displayed a higher variability in the transcriptomic data as compared to the other samples. The TURBO DNA Free treatment affected the RNA samples negatively, decreasing the RNA yield and reducing the quality and reproducibility of the transcriptomic data. We conclude that automated extraction systems should be preferred over manual extraction systems for data consistency, and that the TURBO DNA Free treatment should be avoided when working on RNA samples isolated manually from small volumes of blood.</p><h2>Other Information</h2><p dir="ltr">Published in: Scientific Reports<br>License: <a href="https://creativecommons.org/licenses/by/4.0" target="_blank">https://creativecommons.org/licenses/by/4.0</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1038/s41598-023-30629-5" target="_blank">https://dx.doi.org/10.1038/s41598-023-30629-5</a></p><p dir="ltr">Additional institutions affiliated with: Integrated Genomics Services - Sidra Medicine</p>2023-03-03T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1038/s41598-023-30629-5https://figshare.com/articles/journal_contribution/Technical_assessment_of_different_extraction_methods_and_transcriptome_profiling_of_RNA_isolated_from_small_volumes_of_blood/25125599CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/251255992023-03-03T03:00:00Z |
| spellingShingle | Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood Mahesh Kumar Reddy Kalikiri (17886695) Biological sciences Biochemistry and cell biology Bioinformatics and computational biology Genetics Transcriptome profiling Biomarkers Finger-stick blood collection systems Non-invasive sampling Blood extraction methods RNA isolation Tempus Spin RNA Isolation kit Transcriptomic data Illumina NextSeq 500 system Gene expression data RNA Gene expression profiling RNA integrity number (RIN) RNA-seq data analysis |
| status_str | publishedVersion |
| title | Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood |
| title_full | Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood |
| title_fullStr | Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood |
| title_full_unstemmed | Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood |
| title_short | Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood |
| title_sort | Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood |
| topic | Biological sciences Biochemistry and cell biology Bioinformatics and computational biology Genetics Transcriptome profiling Biomarkers Finger-stick blood collection systems Non-invasive sampling Blood extraction methods RNA isolation Tempus Spin RNA Isolation kit Transcriptomic data Illumina NextSeq 500 system Gene expression data RNA Gene expression profiling RNA integrity number (RIN) RNA-seq data analysis |