Optimizing total RNA extraction method for human and mice samples

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Bioinformatics and Genomics

Main article text

 

Introduction

Material and Methods

Experimental materials

Experimental reagents and instruments

Reagents

Instruments

Experimental Methods

Preparation of tissue samples

Preparation of cell samples

Preparation of blood samples

Total RNA extraction using the TRIzol method

Optimization of the amount of GITC and SDS additions

Total RNA extraction using the GITC-T method

Total RNA extraction using the SDS-T method

Total RNA yield and purity assay

Total RNA integrity assay

Abundance detection of transcripts in total RNA samples

Transcriptome and whole transcriptome sequencing

Statistical analysis

Results

Higher yield of total RNA from animal samples extracted by the GITC-T method

Higher purity of total RNA from animal samples extracted by GITC-T method

Higher integrity of total RNA extracted by the GITC-T method

There is no difference between the total RNA extracted by the GITC-T method and the TRIzol method

The total RNA transcript abundance of animal samples extracted by the GITC-T method was higher

The total RNA extracted from animal samples by the GITC-T method was superior to the TRIzol method

Discussion

Conclusions

Supplemental Information

Comparison of RNA integrity between different sample types

(A) RNA electrophoresis patterns of different samples extracted by the Trizol and GITC-T methods. (B) The intensity ratio of 28S to 18S in (A) was statistically compared to reflect the difference in the integrity of RNA extracted by the GITC-T and Trizol methods.

DOI: 10.7717/peerj.18072/supp-1

Quantify the transcript abundance of the GAPDH and PIRAT1 genes in total RNA samples extracted using different methods

Based on the q-PCR results from Fig. 5B, statistical analysis of the three sample groups shows that gDNA residues are present in the total RNA extracted by both methods. However, the GITC-T method has relatively less residual gDNA, resulting in little impact on the GAPDH (upper panel) and PIRAT1 (lower panel) genes Ct values between the groups with and without gDNA removal. On the far right is the electrophoresis image of the q-PCR products for the GAPDH and PIRAT1 genes, which visually illustrates the impact of residual gDNA in the total RNA samples.

DOI: 10.7717/peerj.18072/supp-2

Denaturing agarose gel electropherogram of total RNA from animal samples obtained by different extraction methods

DOI: 10.7717/peerj.18072/supp-3

List of reagents used in this study

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List of instruments used in this study

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List of primers for q-PCR

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System of real-time fluorescence quantitative PCR reaction

DOI: 10.7717/peerj.18072/supp-7

Total RNA quantity and purity were extracted from samples of different samples

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Author checklist

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Concentration and purity RNA data

DOI: 10.7717/peerj.18072/supp-11

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Yumei Zeng performed the experiments, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Xiaoxue Tang performed the experiments, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Jinwen Chen analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Xi Kang analyzed the data, prepared figures and/or tables, and approved the final draft.

Dazhang Bai conceived and designed the experiments, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

the Ethics Committee of the Affiliated Hospital of North Sichuan Medical College.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

the Animal Research and Ethics Committee of North Sichuan Medical College.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The sequences are available at NCBI: PRJNA1111442.

http://www.ncbi.nlm.nih.gov/bioproject/1111442.

Data Availability

The following information was supplied regarding data availability:

The sequences are available at NCBI: PRJNA1111442.

The RNA-seq data are available at figshare: Bai, Dazhang (2024). Optimizing Total RNA Extraction Method for Animal Tissues. figshare. Dataset. https://doi.org/10.6084/m9.figshare.25678368.v1.

Funding

This work was supported by the Doctoral Research Foundation of North Sichuan Medical College (CBY21-QD17); the City-School Science and Technology Strategic Cooperation Project of Nanchong (22SXQT0032); the Natural Science Foundation of Sichuan Province, Sichuan Science and Technology Program (2023NSFSC0709). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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