2.1 BioProject & BioSample

Introduction

Registering project and biological samples at the K-BDS BioProject and the BioSample databases is a prerequisite for any public KRA submission. The BioProject and BioSample databases store data that relate to organizational and biological aspects of sequencing experiments.

However, for human-derived material data (KHBDB), do not create BioProject or BioSample; instead, follow the KHBDB's guidelines.

BioProject submission describes the goal of the sequencing study, whereas BioSample submission records the nature of the biological material that had been sequenced

BioProject Submission Quick guide

BioProject describes the goal of your research effort. Each study is limited to a single database submission in K-BDS, aligning with the policy that only one data type can be registered per project. you may accumulate data that are suitable for submission in multiple K-BDS databases. To be eligible for KRA submission the project (1) must exist; (2) should not be an umbrella project

1. Log in first to register the BioProject.

2. Click on the BioProject in Submit menu of KRA main page

3. Enter entire section of the BioProject divided into 7 parts. Be sure to fill in fields marked with an asterisk(*)

   1. Project type

   2. Data type (Genomics data - NGS data)

   3. Group information

   4. Submitter

   5. General information of the project

   6. Grant information

   7. Publication and patent

4. Click on the Save at the bottom of the screen after completing the writing

   1. All fields of the BioProject must be entered in English/numbers, and required fields must be filled out

   2. If this requirement is not satisfied, it will not be saved and the screen will be moved to the field that need to be corrected, with the reason for the failure indicated below each field

5. Clink on the Submit to complete your submission

6. When the BioProject is submitted, you can check the submitted content in My submissions of My data of My page or submit the BioSample.

7. When creating BioProject, a temporary number (PSUB#) is assigned and changed to a accession number (KAP#) at the time of approval

8. Please refer to BioProject Documentation for details

BioSample Submission Quick guide

BioSample is a record of biological isolate with unique physical properties. Biological and technical replicates (in most cases) should not be considered unique BioSamples.

Examples:

• 23,000 unique 16S amplicons from a single seawater collection point – 1 BioSample (1 sample was collected and then analyzed to deduce 16S diversity)

• 3 "identical" transgenic mice treated with the same drug as part of an experiment – 1 BioSample

• CHO cells infected with a virus and sampled at 0, 2, 4, and 8 hours post infection – 4 BioSamples (4 time points)

• RNA-Seq data from a single male anteater taken from the brain, heart, lungs, testes, and liver – 5 BioSamples (5 different tissues isolated)

Majority of KRA submissions require more than one sample. Make sure that organism/metagenome, tissue type, time point, etc., have their own sample. Select most appropriate taxonomy for organism/metagenome in the NCBI Taxonomy browser. Providing the exact and most specific name for the organism/metagenome will simplify your BioSample submission. For metagenome or environmental samples look up appropriate taxonomy in the NCBI Taxonomy browser Unspecified sequences taxonomy.

1. Log in first to register the BioSample.

2. Click on the BioSample in Submit menu of KRA main page

3. Enter entire section of the BioSample divided into 3 parts. Be sure to fill in fields marked with an asterisk(*)

   1. BioProject information

   2. Release date

   3. Sample type & Attributes

      1. Select most appropriate sample type

      2. Download Excel template (attributes), fill it out, upload the file

Prerequisites of sample type & attributes

• The sample type consists of a total of 9 types (Human, organism or animal, Invertebrate, Plant, Microbe, Virus, Clinical or host-associated pathogen, Environmental food or other pathogen, Metagenome or environmental)

• Excel template is different for each sample type, so care must be taken when writing metadata

• Each sample name must be meaningful and unique within linked BioProject. Please do not name sample by your sequence data filename

1. Click on the Save at the bottom of the screen after completing the writing

   1. All fields of the BioSample must be entered in English/numbers, and required fields must be filled out

2. Clink on the Submit to complete your submission

3. When the BioSample is submitted, you can check the submitted content in My submissions of My data of My page or submit the KRA.

4. When creating BioSample, a temporary number (SSUB#) is assigned and changed to a accession number (KAS#) at the time of approval

5. Please refer to BioSample Documetation for details

Contact K-BDS staff

If you need assistance or updates regarding BioProject and BioSample submission, please send an email to [e-mail]