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:

1. A Metadata spreadsheet containing descriptive information and protocols for the overall experiment and individual Samples. If submitting a new NimbleGen Platform*, also provide relevant Platform metadata (see templates below).
2. A Matrix spreadsheet containing the final processed/normalized data used to draw the conclusions from your study (e.g., RMA-normalized signal intensities, scaled log2 ChIP/Input ratios). If submitting a new NimbleGen Platform*, also include Platform annotation columns.
3. Raw data files (e.g., .pair).
4. If submitting a new NimbleGen Platform*, please supply native array description files (e.g., .ndf, .pos, .ngd).

* Finding the Platform

On the metadata spreadsheet you are asked to specify what array (Platform) you used. Most commercial Nimblegen Platforms are already represented in GEO, to find the accession number (GPLxxx) use the FIND PLATFORM tool. If submitting a new or custom Nimblegen array, please include all native array description files ((e.g., .ndf, .pos, .ngd) in your archive submission.


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 spreadsheets, including a metadata template, and metadata and matrix examples. Click the tabs at the bottom of the spreadsheet window to switch between spreadsheets. Guidelines for the content of each field is provided on the spreadsheets.

gene expression data

gene expression data with new Platform

genomic data (e.g., aCGH, ChIP-chip)

genomic data with new Platform

Bundle all components (Excel metadata file, raw files, platform description files, and processed matrix table) together into a .zip, .rar, or .tar archive using a program like WinZip, and transfer to GEO by selecting the 'GEOarchive' option on the Direct Deposit page. Incomplete submissions will result in processing delays.