NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.

GEO submission instructions

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Steps

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 geo@ncbi.nlm.nih.gov::

  • 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#####.

FTP Tips

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).