NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.
GEO submission instructions
1. To submit data to GEO, use the instructions here: http://www.ncbi.nlm.nih.gov/geo/info/seq.html#seqdeposit
You will use the "GEOarchive spreadsheet format".
- Be sure to look at the example tabs in the spreadsheet
- If you are adding data to an existing series on GEO, you may leave the "SERIES" section in the spreadsheet blank
- You shouldn't send tarred data. Untar all data. Fastqs and other large files can and should be gzipped
- If you are submitting fastq raw data, you do not need to submit alignment bams
- For a new series, you'll need to include the bioproject ID. Put this below the "SRA_center_name_code" field in the SERIES header of the spreadsheet. The ID numbers are below:
human genomic: 63443 human transcriptomic: 30709 human protein: 63447 mouse genomic: 63471 mouse transcriptomic: 66167 mouse protein: 63475
2. Once you have prepared your metadata, processed & raw files, you will use the FTP upload instructions: http://www.ncbi.nlm.nih.gov/geo/info/seq.html#FTP
- GEO indicates that you can zip/tar your entire submission or send an untarred directory. We recommend just sending a directory, it is much easier
(tips for using the FTP are included at the bottom)
3. After uploading files, email email@example.com::
- Identify your submission as ENCODE project data
- Indicate that you'd like to submit to the "ucsc_encode_dcc" account
- Give the names (or location) of the uploaded files
- If you are adding data to an existing series on GEO, include in your email that this data is to be added to GSE#####.
For Linux/Unix, we recommend that you try 'ncftp' with optimized settings as detailed in: ftp://ftp.ncbi.nih.gov/README.ftp
Here is a typical 'ncftp' session:
1. Connect to the server: > ncftp ftp://geo:D0gDAzr0va@ftp-private.ncbi.nih.gov/fasp 2. Set buffer size (optional): > set so-bufsize 33554432 3. Transfer your archive, or an entire directory plus content using: > put archive_name.tar.gz -or- > put -R directory_name
In Windows and Mac OS X we recommend the free client software, FileZilla: http://filezilla-project.org/download.php?type=client
1. Once the FileZilla client is installed, connect using: host ftp-private.ncbi.nih.gov username geo password D0gDAzr0va 2. Drag-n-drop your file(s) or directory into the /fasp directory on the FTP server. When transferring multiple files we prefer that the files be dropped into a directory (i.e. fasp/your_directory).