Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing

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Biochemistry, Biophysics and Molecular Biology

Main article text

 

Introduction

Materials & Methods

Cells

Harvesting samples, RNA isolation, cDNA library construction, and RNA-Seq

Data analysis

Results

Discussion

Conclusions

Supplemental Information

Plots of gene expression levels (FPKM) against cultivation time (days) of 23 common DEGs.

Black filled circles, black unfilled squares, red filled circles, and red unfilled squares indicate the processing lag times of 15, 30, 45, and 60 min, respectively.

DOI: 10.7717/peerj.11875/supp-1

Genes associated with apoptosis.

249 genes with GO terms included “apoptotic” or “apoptosis”.

DOI: 10.7717/peerj.11875/supp-2

Additional Information and Declarations

Competing Interests

Tomoko Matsuda is an employee of a commercial company: Nihon BioData Corporation.

Author Contributions

Tomoko Matsuda conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The CHO-S cell sequences described here are available at Sequence Read Archive (SRA)/European Nucleotide Archive (ENA)/DDBJ Sequence Read Archive (DRA): DRA006016.

Funding

The authors received no funding for this work.

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