Standard Operating Protocols (SOP)

Requirements for all data set providers

We encourage you to provide us a detailed INFO file view sample along with your data set. This could be a html file (recommended) or a word document with the following information:

• Summary. It would be a brief statement of the main features of this particular data set.
• About the cases used to generate this set of data.
• About the tissue used to generate these data.
• About the array platform.
• About data processing.
• Data source acknowledgment.
• Contact address.
• References.
• Information about this text file.

Once you provide us with an INFO file, we are ready to UploadingDatasetsIntoMySQL.

You may also want to review our DataAnalyzer tool.

Protocols and Procedures for Data Set Processing and Entry in GN MySQL (by Arthur for Arthur)

We encourage you to provide us a detailed INFO file view sample along with your data set. This could be a html file (recommended) or a word document with the following information:

• Get information on this data set from provide (e.g., Rob, Lu, Mike Miles, etc). What species, what tissue, what type of data (expression data, classic phenotypes, genotypes, SNPs). .
• Get information about the cases used to generate this set of data
• About the tissue used to generate these data.
• About the array platform.
• About data processing.
• Data source acknowledgment.
• Contact address.
• References.
• Information about this text file.

* Check strain type using a set of Mendelian transcripts and standard genotype data for certain array data types (e.g., BXD or HXB RI data) * Check sex using Xist and other sex-specific genes for all animal array data (human, mouse, rat, etc.) and some plant data (Arabidopsis and Barley) * Compute mean and range for array data sets and enter into GN for Advanced Search. * Make Table of cases for INFO file. * Compute QTL Reaper data and enter into MySQL. * For every new data set entered in GN, open the INFO file and if it is empty then add text that says who should write the INFO file (e.g. "Data entered by A Centeno, Sept 5, 2008. (Add names of files on GN Quad Xeon or other computer that were actually entered into GN with full path name.) Rob to write the Information INFO file for this data set." * More information about this text file. * More information about this text file. * More information about this text file.

Step by step documentation to perform platform annotation upgrades using BLAT and PERL

Click the link to start the tutorial. PlatformAnnotationUpdatesTutorial

-- ArthurCenteno - 18 Apr 2007