RNA Integrity Database (RINdb)
The RNA
Integrity Database (RINdb) is a free, open-access collection of bioanalyzer sample records each containing curated
information (electropherogram, sample source, extraction method, quality
metrics, and additional metadata). Any user can query the RIN database to
compare results and data, prescreen new experimental methods, and/or view what
RNA sample attributes their peers are obtaining, validating, and using in their
particular applications. Any user can also contribute his or her entries.
RNA
Integrity Number (RIN)
The RNA Integrity Number (RIN) is designed to help scientists estimate the total
RNA integrity of eukaryote samples. Samples that have been run on an Agilent
2100 bioanalyzer are automatically assigned an integrity classification from 10
(intact RNA) to 1 (highly degraded) by the 2100 bioanalyzer expert software.
This classification scale is non-linear (e.g. a sample with a RIN of 2 does NOT
have an average transcript size that is half that of a sample with a RIN of 4).
Because the software-assigned RIN is completely independent of sample concentration,
instrument, and analyst, it is a reproducible, consistent, and robust assessment
tool. As the integrity tolerance of any experiment relies upon numerous variables
(e.g. assay type, probe, primer, amplicon length, experimental design, etc.), Agilent
highly recommends that a suitable RIN threshold be experimentally determined
and validated for any new conditions.
RNA Integrity Database (RINdb) Administration
Forum
The
RINdb Administration Forum is the group of scientists and individuals that regularly
meet to drive future changes to the RINdb – its architecture, web interface,
and associated tools. Individuals and/or organizations interested in participating
in the Administration Forum should contact the database administrator for more
information.
What types of queries
can I perform on the RINdb?
Simple query: An illustrative
example of an actual electropherogram specific to a particular sample type and
quality. Additional quantitative and qualitative metadata from quality metrics
permits direct comparison of sample types (i.e. fresh versus frozen), isolation
kits (Manufacturer A versus B), etc.
Advanced queries: As the number of records,
content, and statistical tools associated with the RINdb increases, advanced
queries will be enabled. Future tasks include measuring the effects of standard
RNA metrics in the quality metrics of a downstream gene expression experiment and
in silico evaluation of extraction kits
and other sample preparation consumables.
Figure 1: RINdb usage point in the Gene Expression (GE)
workflow
Is the RINdb proprietary?
No.
All RINdb information is explicitly contributed by and for the use of the
scientific community at large. To address confidentiality issues, submitters have
the option of removing sensitive information (e.g. internal sample names, organization
affiliation, contact information, etc.).
Is RINdb content reviewed prior to upload? By whom?
Yes.
Agilent has a team of scientists reviewing and curating all content
submissions, from new entries to entry comments. This team consists of experienced
users within the Bioanalyzer RNA community paired with Agilent scientists. Team
curators regularly participate in the RINdb administration forum (see “Definitions”
section).
How does the query function work?
In
general terms, the keyword search links all keywords with an “OR” logical operator.
The pull down menu entry uses the “AND” operator to limit the number of entries
a search returns. We recommend users rely upon the automated pull down menus
for query restriction when there is no interest in dissimilar entries. The
keyword search looks in all entry fields.
Can I sort the entries in my
query results?
Yes.
Entries can be sorted by various numerical values such as search relevance,
RIN, ribosomal ratio, UV 260/280 ratio, RNA concentration, or latest
modification date. The default sorting value is “relevance”, followed by “RNA
integrity Number (RIN)”.
I cannot find the exact
sample I am looking for. What do I do?
Cohorts
such as sample types or RNA isolation kits generally behave similarly. We
recommend users create initial queries that are generic, review the returned
entries, and then refine queries further to obtain a more specific fit. Keep in
mind that relevant information may not reside within a single entry, but in the
common properties of a particular sample type. If you do have a sample type
example not yet documented within the RINdb, consider contributing it.
I found the same type of
sample in the database, but my results are different. Now what?
If
your results are of poorer quality:
-
Consider reviewing references for more information (such as successful methods).
- Contribute a detailed comment for the specific entry.
-
If the original submitter has allowed it, you can directly email him or her questions.
If
your results are of higher quality:
-
Consider contributing an example entry of your results into the RINdb.
-
If you feel that an entry or data in the RINdb may be misleading or invalid,
please contact the database curator.
The option “send message to
author” appears on some but not all entries. Why is this?
During
the submission process, submitters can freely designate whether they want to be
directly contacted by other RINdb users regarding their specific entries.
I want to contribute to the
RNA integrity database. How do I find out if my samples are relevant?
The
intent of the RINdb is to house a collection of hundreds–thousands of real
sample examples, covering all possible sources, and storage and isolation
conditions. Duplicate entries are allowed but curation will limit excessive
postings.
I’d like to submit a large number
of samples. Is there a batch upload option?
Yes.
You can download a content template for
larger number of samples. We recommend you contact the database administrator when you
have a few entries collected to verify that your format and content are
appropriate.
Why do I need to register to
submit an entry?
Registration
is used to help link the entries to their original submitter, allowing he or she
continual access for purposes of making modifications or responding to
submitted comments and queries (through the database administrator).
My company/institution
policies do not allow me to share sensitive data.
Bioanalyzer
RNA traces do not contain gene specific information. You can verify with your
legal department to determine if entry submission (minus sample name specifics,
purpose, etc.) is acceptable. While all contributions must be made by
registered users, the built-in privacy options allow submitters to hide fields
such as name, organization affiliation, and contact information.
Can I change the privacy
options?
Yes.
Submitters have the option of modifying both their privacy options and entries
at any time. Please email the database administrator.