Guide to Illumina Sequencing Submission Forms
Submitting samples for Illumina next-generation sequencing (NGS) is a critical step in ensuring high-quality data output. The submission form serves as the primary communication link between the researcher and the genomics core facility. Accurate completion of this document prevents processing delays, sample mix-ups, and suboptimal sequencing results.
Why the Submission Form Matters
The sequencing submission form captures essential metadata about your biological samples. Core facility staff rely on this information to plan library preparation protocols, determine required sequencing depth, and select the appropriate flow cell chemistry. Even minor discrepancies in information, such as incorrect species identification or inaccurate DNA concentrations, can lead to failed runs or data that does not align with your experimental goals.
Key Information Required
1. Sample Identification and Quality Control
Each sample must have a unique identifier. This ID will appear in your final bioinformatics files, so consistency is paramount. Alongside the ID, you must provide:
- Source/Species: Knowing the organism is vital for choosing the correct reference genome for alignment and for understanding potential bias in GC content.
- Sample Type: Indicate whether the input is genomic DNA (gDNA), total RNA, or a specific library type (e.g., ChIP-seq, ATAC-seq).
- Quality Metrics: Most facilities require a quantification value (e.g., Qubit concentration) and a quality assessment (e.g., RIN score for RNA, or fragment size distribution via Bioanalyzer/TapeStation).
2. Sequencing Parameters
The core facility needs to understand your experimental design to allocate the right amount of "real estate" on the flow cell. This includes:
- Read Length: (e.g., 2x150bp or 1x75bp) determines the resolution of your data.
- Coverage Requirements: How many million reads per sample do you need? This is usually driven by the complexity of the genome or the depth required to detect rare variants.
- Library Configuration: Are you submitting pre-prepared libraries, or do you require the core facility to perform library construction from your raw inputs?
3. Indexing and Multiplexing
If you are pooling multiple samples together, the submission form must clearly list the indexes (barcodes) used for each sample. Incorrect index sequences can lead to "index hopping" or misassigned reads. Ensure that the indexes provided are compatible with the specific Illumina platform being used, such as NovaSeq or MiSeq.
Best Practices for Submission
To expedite the turnaround time, follow these best practices:
- Standardize Concentrations: Always follow the specific concentration requirements provided by the facility. Submitting samples that are too dilute or too concentrated may result in the need for re-normalization.
- Labeling: Ensure labels on tubes match the submission form exactly. Use permanent, chemical-resistant markers or printed labels that can withstand cryogenic storage.
- Storage Conditions: Verify whether your samples should be shipped on dry ice, wet ice, or at room temperature based on their stability.
- Communication: If your samples are precious or difficult to obtain, contact the core facility manager before submission to discuss any specific handling requirements.
Common Pitfalls to Avoid
Incomplete forms are the most common cause of processing delays. Avoid leaving fields blankif a parameter is unknown, contact the facility rather than guessing. Additionally, ensure that your data formatting (such as file names) conforms to the facilitys specific nomenclature requirements to avoid errors during the automated data delivery process.
By treating the submission form as a formal technical document, researchers can significantly reduce the risk of experimental failure and ensure that their sequencing project proceeds from submission to data analysis as smoothly as possible.
