How do I find all instances of a specific study type (e.g. human genomic re-sequencing experiments) in the SRA?

1.

Go to the Entrez SRA page.

2.

Enter human[organism] AND study type resequencing[Properties] AND biomol genomic[Properties] in the search box at the top of the page.

3.

Click the “Search” button.

4.

Your search results will be presented as a list of human genomic resequencing experiments (SRX/ERX/DRX accessions) available in the SRA.

5.

Click on the SRX record of interest. The record will include:

a.

Links to each run in the experiment

b.

Experiment design information

c.

Submission accession and submitter name

d.

Study summary and abstract (if available)

e.

Experiment sample (SRS) information

f.

Links to a list of experiments (SRX)

g.

Library information (if available)

h.

Platform information

i.

Processing information (base calls and quality scores)

j.

Spot descriptor information

k.

Links to related information

6.

At this point, you can do one of the following:

a.

Click on the “All experiments” link for a complete list of the experiments included in the study.

b.

Download the data for a particular experiment by clicking on the SRA or the SRA-lite download links. These links will take you to the SRA FTP site where the files are available for download. If there are no download links for the experiment record, please contact vog.hin.mln.ibcn@ars.

c.

Click on one of the run links (SRR/ERR/DRR accessions) to go to the SRA Run Browser, where you can look at individual reads, search the spots for a specific sequence, or download a set of spots from the run.

Note: Since SRA is a raw data archive (not curated) and can index only those terms that a submitter provides in the metadata of their submission, your search results may not include all possible studies associated with your search term.

Note: If you choose to download files, install the “Aspera Connect” plug-in to transfer files at a significantly faster rate than ftp.