2.1 From the SRA Homepage:

Click the Submit tab.

Then click myNCBI and login with PDA crenditials. (PDA and myNCBI have merged. If you do not have a PDA or myNCBI account already, one will need to be created. If you have used a PDA account in the past but no longer see your previous SRA submissions, please contact SRA at sra/at/ncbi.nlm.nih.gov for assistance with your account view.)

(See Figure 2)

Figure

Figure 2 From the 'Submit' tab, click myNCBI to login for Submission.

3.1 Submission Alias and Comment

Submission ID also known as ‘Alias’ - will be used for tracking within the archive and for the submitter. This field should be something that makes sense to the submitter.

Example: C. elegans resequencing project (this field is NOT indexed in Entrez).

Submission Comment – area for submitter to enter a comment about the submission.

Example: prepared with assistance by John Smith (this field is NOT indexed in Entrez).

(See Figure 4)

Figure

Figure 4 The Submission is not created until the ‘Save’ button is clicked.

4.1 Creating a New Study

A Study identifies the sequencing study or project and may contain multiple experiments.

Study accessions are a good choice as the reference in a scientific journal article because the published Study provides a good landing page for users seeking to download data.

(See Figure 5)

Figure

Figure 5 Create the Study by clicking the button for ‘New Study’.

4.2 Describing a Study

Alias- Used as a reference for the submitter and archive. (NOT an indexed field)

Title- Publicly viewable title. A title from a journal article or other descriptive title should be used.

Study Type- Drop-down menu providing a selection of different categories for sequencing projects. Used as a method for users to find general types of studies. Pick the closest category and avoid ‘other’ if possible.

Abstract- Describes the goals, purpose, and scope of the study.

Description- Allows for more extensive and free-form description of the study.

Project Name- Name used by submitter for the project, if different from the Study Title.

Project ID- Genome Project ID. New Projects can be created here.

Links and Attributes- Used to add URLs, Entrez Links, or other Attributes in a key-value pair configuration. If linking to other databases, please use the correct database abbreviation.

• If the Study accompanies a journal article, enter the PubMed ID (pmid) as an ‘entrez link’ with “pubmed” as the ‘DB’ and the pmid as the ‘ID’.

(See Figure 6)

Figure

Figure 6 The PMID for an article is listed at the bottom of the article’s PubMed Summary.

(See Figure 7)

Figure

Figure 7 Example showing the SRA Interactive Tool (left) compared to the view of the same Study in Entrez (right). Above Study in Entrez

7.1 Creating Samples

Each unique sample used in a study needs to have its own sample object within the submission. The exception to that rule is when samples were intentionally pooled. A pooled sample is one sample but should explicitly describe as much as is known about what was in the pool. Please contact SRA at sra/at/ncbi.nlm.nih.gov for help with barcoded or indexed samples. A Study may contain multiple Samples.

(See Figure 10)

Figure

Figure 10 Click the 'New Sample' button to create a new Sample.

7.2 Describing a Sample

Alias- Used as a reference for the user and archive. (NOT an indexed field)

Title-Publicly viewable title. A formal title used to describe the Sample. If the submission goes along with a journal publication, the title should distinguish samples within the article.

Anonymized Name- Anonymous public name of the sample. For example, HapMap human isolate NA12878.

NCBI Taxon ID- ID number from the NCBI Taxonomy database. For samples that do not have an appropriate Taxonomy entry, the submitter will need to apply for a new Taxon ID.

Description- Allows for more extensive and detailed description of the sample.

Links and Attributes- Used to add URLs, Entrez Links, or other Attributes in a key-value pair configuration. If linking to other databases, please use the correct database abbreviation.

(See Figure 11)

Figure

Figure 11 Samples should be fully described such that a user does not need to find an accompanying publication. The information is not stored until the ‘Save’ button is clicked. Saved samples can be updated as necessary.

8.1 Creating Experiments

Experiment describes the library, platform selection, and processing parameters. Each change to the library or sequencer parameters requires the creation of a new experiment. A Sample can contain multiple experiments but each experiment contains only one library.

(See Figure 12)

Figure

Figure 12 Click the ‘New Experiment’ button to begin creating an Experiment.

8.2 Describing an Experiment

8.2.3 Processing

This section varies with the sequencer selected. Please pay close attention to the answers provided in this section, as they may affect proper loading of data.

Links and Attributes- Used to add URLs, Entrez Links, or other Attributes in a key-value pair configuration. If linking to other databases, please use the correct database abbreviation.

(See Figure 13)

Figure

Figure 13 Click the 'Save' button to store the Experiment information. Saved Experiments can be updated as necessary.

9.1 Creating Runs

Runs describe the files that belong to the previously created Experiments. Runs are divided by production run of the sequencer. Experiments may contain many Runs depending on how many sequencer runs were involved in data acquisition.

(See Figure 14)

Figure

Figure 14 Click the 'New Run' button to the right of the Experiment for which a Run is needed. Each Experiment will have its own ‘New Run’ button.

9.2 Describing a Run

Alias- Used as a reference for the user and archive. (NOT an indexed field)

Run data file type- The storage format (srf, sff, fastq, etc) of the sequence data being submitted. More information about the file types currently accepted by the SRA can be found in the SRA Submission Guidelines.

File Name- Name of the file transferred to the SRA including any file extensions. Data files contained in a .tar archive need to be individually enumerated in a run.

MD5 checksum- A checksum or hash sum generated for the file listed in ‘File Name’ that is used to detect errors introduced through storage or transfer. SRA uses the file name and md5 checksum to track and link files to their proper Runs.

Unix-  md5sum <file>
OS X- md5 <file>

Windows- Application required. Fsum Frontend(Please use Base16 for md5sum calculations) and WinMD5Sum are two possible options.

Plate and Region- Only seen on certain file types like FASTQ. Because some file types have limited addressing information, these fields allow the user to provide the address information for the sequencing media used.

(See Figure 15)

Figure

Figure 15 Click the 'Save' button to store the Run information. Runs can only be updated until data has been loaded for the Run. Once there is data in a Run, it will be locked from further updates. Contact SRA for changes to be made to locked Runs.