Bulk RNA-seq meta-data standards

Bulk RNA-sequencing

This document describes meta-data standards in PanKbase for reporting bulk RNA-sequencing studies

Overview

Bulk RNA-sequencing (RNA-seq) produces genomic sequencing data describing the abundance of RNA transcripts in a biosample from RNA molecules such as protein-coding and long non-coding RNA transcripts.

I. Meta-data collection standards

For each RNA-seq experiment, a series of meta-data should be collected for both the experiment as well as the donor and biosample that the experiment was generated from.

Donor - meta-data describing the donor that the biosample was obtained from

Biosample - meta-data describing the biosample that the assay was performed on, including:

• Type of biosample (e.g. tissue, cell line etc.)
• Biosample ontology term
• Treatments or genetic modifications used
• Fraction or other derivation from another sample (if applicable)
• Abundance of starting material for the sample
• Information about sample obtained from a supplier (if applicable)
• Protocol and methods used to culture sample
• Validation of cell line or for tissue fidelity

RNA preparation - meta-data describing the type of RNA preparation performed, including:

• Type of preparation (e.g. total RNA, poly-A RNA)
• Size of RNA fraction
• Description of any kits used for example for ribo-depletion

RNA isolation

• Document including more detailed information about RNA isolation protocol including isolation methods, depletion, selections and any treatments

RNA quantification and QC - meta-data describing:

• Quantification and quality control of RNA preparation

Library construction - meta-data describing the library created from RNA preparation including:

• Library preparation kit (or protocol if a custom method)
• Library stranded or unstranded
• Description of any metrics used to assess library quality

Sequencing - meta-data describing the sequencing of the library including:

• Platform used (e.g. Illumina HiSeq)
• Type of sequencing (single or paired end)
• Read length
• Description of any barcoding used

Experimental design - meta-data describing the design of the experiment including:

• Technical replicates
• Biological replicates