Data Submission to dbGaP¶
The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans.
The ERCC Data Coordination Center developed this wiki to guide ERCC members on how to submit their data to dbGaP or GEO, after they have submitted their data to the exRNA Atlas.
- Data Submission to dbGaP
- Full Submission Guide From dbGaP
- Understanding the Process of Data Submission to dbGaP
- Register Your Study
- Fill Out the Study Config
- Fill Out the Phenotype Data
- Molecular Data Submission
- High Throughput Sequencing Submission
- Fill Out the Sequence Metadata File
- Upload Sequence File
- Confirm and Release the Study
To submit your data to dbGaP, follow these six steps:
1. Register the study
2. Fill out study config
3. Create phenotype data
4. Create sequence metadata file
5. Upload sequence file
6. Confirm and release the study
Please contact the ERCC DCC at brl-exrna@bcm.edu if any assistance is needed and we can help with steps 4-6.
We will need to be assigned as submitter for the study (the PI will have the option to do so after the study has been registered), and a completed submission to the exRNA Atlas.
Full Submission Guide From dbGaP¶
Understanding the Process of Data Submission to dbGaP¶
Register Your Study¶
Finding the Genomic Program Administrator (GPA) and registering the study.
Fill Out the Study Config¶
What is the Study Config?
Here is a study config file with required areas highlighted in yellow.
Fill Out the Phenotype Data¶
Subject Consent Files
Sample Mapping Files
Pedigree Files
Subject Phenotypes Files
Sample Attributes Files
Molecular Data Submission¶
Molecular data should be submitted to the dbGaP Submission Portal under the section "Other files" with type "Molecular Data". It should be submitted along with the phenotype data.
For more information and other requirements, here is the FAQ from dbGaP
High Throughput Sequencing Submission¶
Fill Out the Sequence Metadata File¶
Once the previous files have been validated by dbGaP, the dbGap curator will reach out and provide the sequence metadata file to be filled and returned.- Instructions are provided in the sequence metadata file.
Upload Sequence File¶
The sequence metadata file will have to be validated by dbGaP first and then the dbGaP curator will send the information on where to submit the sequence files.
Confirm and Release the Study¶
The dbGaP curator will provide preview of the study and make sure everything is correct prior to release it on dbGaP.