Recommendations for Nimblegen submissions
This page contains deposit recommendations, instructions and templates specific to Nimblegen arrays. These recommendations simply describe what we believe is the easiest batch deposit method for the majority of Nimblegen researchers, but keep in mind that Nimblegen 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.
The GEOarchive spreadsheet-based submission method is recommended for Nimblegen 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.
- A Matrix worksheet containing the processed/normalized data used to draw conclusions from your study (e.g., RMA-normalized signals, scaled log2 ChIP/Input ratios, etc.). If the processed data row count exceeds Excel's limit, please supply your Matrix as a tab-delimited, plain-text file (.txt). Alternatively, if your data were processed with Nimblescan software, the processed data may be supplied as native .gff files.
- Raw data files (e.g., .pair).
Finding the Platform
On the Metadata worksheet you are asked to specify what array (Platform) you used. Many NimbleGen Platforms are already represented in GEO; to find the accession number (GPLxxx) use the FIND PLATFORM tool. If you are using a commercial (catalog) array not yet represented in GEO, please e-mail us the array title and design details (Example: Human CGH 2.1M Whole-Genome Tiling Array, design name: 080131_HG18_WG_CGH_v2D_HX1, design id: 6612) and we will create an official NimbleGen Platform record. If you are using a custom array not yet represented in GEO, please include all design files (.ndf, .pos, .ngd, etc.) in your GEOarchive submission. Please also include custom Platform descriptive details in the Metadata worksheet and custom Platform annotation columns in the Matrix worksheet or in a .txt file.
Nimblegen GEOarchive templates and examples
The following Excel files illustrate the structure of different types of GEOarchive Nimblegen data submissions. Each Excel file consists of several worksheets, including a metadata template, and metadata and matrix examples. Click the tabs at the bottom of the spreadsheet window to switch between worksheets. Guidelines for the content of each field is provided on the worksheets.
- gene expression data
- gene expression data with new custom Platform
- genomic data (e.g., aCGH, ChIP-chip)
- genomic data with new custom Platform
Bundle all components (Excel Metadata file, Matrix or processed data files, raw data files, and custom Platform design files if appropriate) 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.