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SRA Knowledge Base [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2011-.

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SRA Knowledge Base [Internet].

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Searching for Data Generated by a Specific Platform or Instrument

.

Can I search for SRA data by platform/instrument type?

Yes, you can search SRA for data by platform/instrument type using Entrez SRA.

  • Search for the platform/instrument type by placing quotation marks around the name of the platform/instrument (e.g. “ab solid system 3 0”) or by using a qualifier at the end of a compound word (e.g. ab solid system 3 0[word] or ab solid system 3 0[all]).
  • If you search for an unquoted or unqualified phrase (e.g. ab solid system 3 0), Entrez will not treat the words as a name – they will be treated as list of words joined by the Boolean operator AND. This means Entrez will search for each of the words in all fields irrespective of order, and your search results may contain records that would not normally be included in the results of a search for the name of the platform/instrument type.
  • To see how Entrez interpreted your query, look in the “Search Details” text box on your result page.

Your search results will be presented as a list of experiments (SRX/ERX/DRX accessions) whose metadata contains the phrase you entered in the query box.

1.

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

a.

Links to each run in the experiment

b.

Experiment design information (if available)

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

2.

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

a.

Click on the “All experiments” link to see 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: Search results may not include all studies that used the specified platform or instrument 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.

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

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