4) Procedure

The following steps outline the procedure for the preparation of samples for omics-based studies:

1. Step 1: Sample Collection
   1. Collect samples according to the study protocol, ensuring that appropriate consent is obtained for human or animal samples, as applicable.
   2. Use standardized collection procedures to minimize variability between samples. Document the collection date, sample source, and collection method for traceability.
   3. Ensure that samples are collected under appropriate conditions to prevent contamination or degradation (e.g., use sterile collection tools, maintain proper temperature during transport).
2. Step 2: Sample Labeling and Documentation
   1. Label each sample clearly with relevant information such as the study ID, sample type, collection date, and sample identifier (e.g., barcode or unique ID).
   2. Ensure that each sample is logged into the laboratory information management system (LIMS) or tracking database with accurate documentation of its collection and handling history.
   3. Maintain a sample logbook or electronic record to track sample location, condition, and any handling steps performed during the preparation process.
3. Step 3: Sample Processing
   1. Prepare samples according to the specific omics technology to be used (e.g., RNA extraction for transcriptomics, protein extraction for proteomics, or metabolite extraction for metabolomics).
   2. Ensure that all reagents and consumables used for sample processing are of high quality and free from contamination.
   3. Follow the validated protocols for sample extraction, avoiding cross-contamination between samples. Ensure that all equipment is calibrated and maintained regularly.
   4. If applicable, process samples in replicates to ensure that biological variation is captured.
4. Step 4: Sample Quality Control
   1. Perform quality control (QC) checks on processed samples to ensure that they meet the required specifications for omics analysis. This may include checking for sample concentration, purity, and integrity using methods such as spectrophotometry, gel electrophoresis, or mass spectrometry.
   2. Verify that the processed samples are of sufficient quantity and quality to support downstream omics analyses. Document all QC results for traceability.
5. Step 5: Sample Storage
   1. Store prepared samples according to the appropriate storage conditions (e.g., -80°C for long-term storage, room temperature for short-term storage) to preserve sample integrity.
   2. Ensure that samples are stored in clearly labeled containers with sufficient information to identify the study, sample type, and storage conditions.
   3. Use dedicated freezers or storage areas for samples to avoid contamination or degradation due to environmental factors such as temperature fluctuations.
6. Step 6: Sample Transport (if applicable)
   1. If samples need to be transported to external labs or collaborators, ensure that they are packaged and shipped according to relevant regulations, using proper labeling and tracking.
   2. Maintain a chain of custody for each sample to ensure that it is tracked and handled appropriately during transport.
7. Step 7: Documentation and Record Keeping
   1. Ensure that all sample handling activities, including collection, processing, QC checks, storage, and transport, are documented accurately and consistently in study records.
   2. Maintain a sample tracking log that includes the sample ID, processing dates, QC results, and storage conditions. This log should be easily accessible for review or audit purposes.
8. Step 8: Sample Disposal
   1. Dispose of any samples that are no longer required or have expired according to biosafety and environmental regulations. This may involve biohazard disposal for biological samples or chemical waste disposal for reagents and solvents.
   2. Ensure that the disposal process is documented, including the method of disposal and the reason for sample disposal.

5) Documents

The following documents should be maintained during the preparation of samples for omics-based studies:

1. Sample Collection Logs
2. Sample Processing Protocols
3. Quality Control Checklists and Results
4. Sample Tracking Logbooks
5. Storage and Transport Records
6. Sample Disposal Logs

6) Abbreviations

• QC: Quality Control
• LIMS: Laboratory Information Management System
• RNA: Ribonucleic Acid
• DNA: Deoxyribonucleic Acid
• FBS: Fetal Bovine Serum

7) References

References to regulatory guidelines and scientific literature that support this SOP:

• OECD Guidelines for Good Laboratory Practice (GLP)
• FDA Guidelines for Preclinical Safety Testing
• ICH E6 Good Clinical Practice Guidelines
• International Standards for Omics Data Collection

8) Version

Version 1.0: Initial version of the SOP.

9) Annexure

Sample Processing Log Template