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Documentation for data submissions

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Documentation is required for each data type (e.g. ChIP-seq, RNA-seq). The documentation is developed as part of the data agreement, before data are submitted. The primary document for a datatype, the track description, (example here) is displayed in the Genome Browser when the track title is clicked. Required sections are listed below.

1. Description

  • Describes experiment goals and significance. Includes biological background necessary to understand the data.
  • Should be written by the PI or someone with comparable expertise and writing skills, targeted at a general biomedical audience.
  • Should be between one and five paragraphs long, and similar in content to the abstract of a scientific paper describing the data.

2. Methods

  • Describes experimental methods. Written at a relatively high level, as for the methods section of a biomedical research paper. Should mention sample preparation, assay, and analysis programs. Include specific information where it is of general interest, such as sequencing system used, and program names for peak calling software. A general or summary description of the following aspects of the experiment may be included in the Methods, and full details can be included in the Protocols section, below.
 - Sample preparation
   * isolation
   * amplification
   * enrichment
   * partitioning

 - Sequencing system used, parameters and run-time settings

 - Processing and analysis software used
    * program name
    * version
    * algorithm description
    * parameters
  • Written so that a specialist in the area can understand
  • May refer to more detailed protocols (see below).

3. Release Notes

  • Release N and info as it relates to a previous assembly
  • Information about what makes this release different, added cell lines, added replicates, added veiws

4. Verification

  • The methods that were used to verify the experiment
  • Links to GEO or supplemental Validation data or other tracks

5. Credits

  • Lists contributors to this dataset.
  • A contact email/person is required for each composite track.

6. References

  • Lists relevant publications, in PUBMED citation format.
  • Alphabetical by first author


In addition to the primary documentation (which is required to submit data), supplementary Protocol documents may be provided:

Protocols

  • Describe experimental protocols in detail, including all reagents, quantities, analysis parameters
  • Written so that a comparable lab can reproduce
  • Accessed via link from Methods section of track description


We suggest that the principal investigator(s) for the project prepare the track description, and that the senior experimental and analysis personnel prepare the Protocols document. Protocols are an additional level of documentation useful for ENCODE data submissions, because this data is released to the public via the Genome Browser pre-publication (for published data, this level of detail generally appears in the Materials & Methods of the publication).