Difference between revisions of "How to Submit GBS Data to the NCBI Sequence Read Archive (SRA)"

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Revision as of 14:18, 24 September 2019 (view source) Altschuler (Talk | contribs) (→‎2. Create BioSample) ← Older edit		Revision as of 15:40, 24 September 2019 (view source) Altschuler (Talk | contribs) (→‎2. Create BioSample) Newer edit →
Line 31:		Line 31:
	<li>Submitter</li>		<li>Submitter</li>
	<li>General Info</li>		<li>General Info</li>
−	* Release Date: Check either:	+	* Release date: Check either:
−	* Release immediately following processing or	+	** Select either "Release immediately following processing" or "Release on specified date or upon publication, whichever is first and enter a Projected Release Date."
−	* Release on specified date or upon publication, whichever is first and enter a Projected Release Date.	+	* Specify if you are submitting a single sample or a file containing multiple samples
		+	** Select "Batch/Multiple" or "Single"
	<li>Sample Type</li>		<li>Sample Type</li>
	* Select the Plant Sample check box.		* Select the Plant Sample check box.
	<li>Attributes</li>		<li>Attributes</li>
−	* Sample Name: e.g. Lakin-Fuller RIL Population	+	* Provide your BioSample attributes directly on the screen or by uploading a .csv file.
−	* Organism: e.g. Triticum aestivum	+
−	* Cultivar:e.g. Lakin-Fuller	+
−	* Development Stage: e.g. Mature Plants	+
−	* Geographic Location: e.g. USA	+
−	* Tissue: e.g. Leaf	+
−	<li>Description</li>	+
−	* Sample Title: e.g. Plant sample from Triticum aestivum Lakin-Fuller RIL population	+
−	* Public Description: Optional additional descriptive information	+
	<li>Review & Submit</li>		<li>Review & Submit</li>
	* Check that all of the information displayed is correct and make any necessary adjustments. Then click Submit to submit the BioSample.		* Check that all of the information displayed is correct and make any necessary adjustments. Then click Submit to submit the BioSample.

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Revision as of 15:40, 24 September 2019

There are three steps in submitting sequence data to the NCBI Sequence Read Archive (SRA):

1. Create a BioProject

Login to the NCBI Submission Portal: https://submit.ncbi.nlm.nih.gov/subs/bioproject/ and click on New Submission. Then fill out the following sections. After each section, click “Continue” to move on to the next section:

1. Submitter
2. Project Type
• Project data type: Check “Phenotype or Genotype.”
• Sample scope: “Select Multiisolate.”
3. Target
• Organism name: e.g. Triticum aestivum
4. General Info
• Release date: Choose either “Release immediately following processing” or “Release on specified date or upon publication, whichever is first” and enter a Projected release date.
• Project title: Enter a title of your choosing.
• Public description: Provide a paragraph of the study goals and relevance.
• Is your project part of a larger initiative which is already registered with NCBI? Select Yes or No. If yes, enter the "Initiative description" and the "BioProject accession" of the larger initiative to which this project belongs.
5. BioSample
• Click on “Continue.” You will be able to create a BioSample after you finish creating this BioProject.
6. Publications
• Enter a PubMed ID or DOI if available.
7. Review & Submit
• Review all the information and click “Submit” if everything looks ok. If anything looks wrong, you can go back to any section by clicking on its respective tab at the top.

2. Create BioSample

Login to the NCBI Submission Portal: https://submit.ncbi.nlm.nih.gov/subs/biosample/and click on New Submission. Then fill out the following sections. After each section, click “Continue” to move on to the next section:

1. Submitter
2. General Info
• Release date: Check either:
  • Select either "Release immediately following processing" or "Release on specified date or upon publication, whichever is first and enter a Projected Release Date."
• Specify if you are submitting a single sample or a file containing multiple samples
  • Select "Batch/Multiple" or "Single"
3. Sample Type
• Select the Plant Sample check box.
4. Attributes
• Provide your BioSample attributes directly on the screen or by uploading a .csv file.
5. Review & Submit
• Check that all of the information displayed is correct and make any necessary adjustments. Then click Submit to submit the BioSample.

3. Create Sequence Read Archive Submission