Recommendations for real time PCR submissions
This page contains deposit recommendations, instructions and a template specific to quantitative RT-PCR deposits. These recommendations describe what we believe is the easiest batch deposit method for the majority of researchers, but keep in mind that RT-PCR data may be submitted to GEO using any of the deposit options described on the Submitting data page. If you need additional guidance for your submission, please e-mail us with a brief description of the type of data you are trying to submit, and one of our curators will quickly get back to you.
Please understand that GEO hosts high-throughput data submissions that cannot be easily represented within the body of published manuscripts. Generally, we consider RT-PCR analysis of over 50 genes to be high-throughput, but if you have a moderate number of samples (over 20), we will accept submissions with as few as 20 genes.
The GEOarchive spreadsheet-based submission method is recommended for RT-PCR deposits.
With this submission option, you provide the following components:
- A Metadata worksheet containing descriptive information and protocols for the overall experiment and individual Samples. If submitting a new RT-PCR virtual Platform (i.e., panel of assays), also provide relevant Platform metadata (see template below).
- A Matrix_non-normalized worksheet containing non-normalized data (e.g., raw Ct values).
- A Matrix_normalized worksheet containing the final processed/normalized signal data used to draw the conclusions from your study (e.g., target gene signal normalized to housekeeping genes). If submitting a new RT-PCR assay panel, also include Platform annotation columns.
- A Fold_Change worksheet containing fold-change data (e.g., test/control).
Finding the Platform
On the Metadata worksheet you are asked to specify the PCR assay panel you used. Many commercial PCR assay panels are already represented in GEO; to find the accession number (GPLxxx) use the FIND PLATFORM tool. If submitting a new PCR assay panel, please include Platform annotation columns in your Matrix_normalized worksheet.
RT-PCR GEOarchive templates and examples
The following GEOarchive template is suitable for RT-PCR submissions based on PCR platforms already in, or new to, GEO. The template consists of eight worksheets: Metadata, Matrix_non-normalized, Matrix_normalized, Fold_Change, and examples. Click the tabs at the bottom of the worksheet window to switch between worksheets. Guidelines for the content of each field is provided on the worksheets.
Bundle all components (Excel Metadata sheet, non-normalized/normalized/fold-change Matrix sheets) together into a .zip, .rar, or .tar archive using a program like WinZip, and transfer to GEO using the Submit to GEO page. Incomplete submissions will result in processing delays.