What is the goal of the MIT/ICBP Database?
How do I submit sequences?
How do I search for a gene of interest?

What is the goal of the MIT/ICBP Database?

The MIT/ICBP siRNA database aims to provide a resource for researchers looking for validated siRNAs against target genes, with an emphasis on genes potentially involved in cancer. Our site has basic information regarding submitted sequences. In addition, we provide links to more annotated information available through NCBI's probe database.

How do I submit sequences?

Sequence submissions are available through our siRNA and shRNA sequence submission pages, Information regarding specific submission fields can be found in our submission quidelines below.

If you have purchased an siRNA/shRNA from a commercial site and validated it yourself, you may also submit that sequence. Please provide the name of the company and any other relevant information on the "comments" field within the Probes section of the submission form.

Sequence submission guidelines

Personal Information

Name
Your name

Email
Primary work email address.

Title
Your research position.

Principal Investigator
Please list the name of your lab's PI.

Department or center
ex. KI, Whitehead Institute, Broad Institute

NCBI Probe Database

Submission status
If you or your colleagues have submitted your siRNA to the NCBI Probes Database previously, please provide the NCBI Probe ID Number so that we may link to your online data.

If you have not submitted your siRNA construct to the NCBI Probes database, we will submit it for you based on your submission data. Once accepted by NCBI, we will provide you with the reference numbers.

Reference

Please provide the Pubmed ID# of your publications that first describe the siRNA sequence you are submitting.

If the article is currently in press, we request that you provide us with the article title, authors, and journal so that we can provide links upon publication.

If the siRNA/shRNA is unpublished or in preperation, you may add a title for your project and/or other researchers names that worked on the validation experiments.

Probes

Probe name
Please provide a name for the siRNA sequence you are submitting.

Target mRNA accession #
Please provide the NCBI accession number for the gene your siRNA targets (NM_ or XM_ numbers preferred). You may search for the accession number on the NCBI website. Please note that you can narrow the search results by clicking the "mRNA" button that appears at the top of you results list.

Target mRNA name
Please provide the name of the gene being knocked down; if it has several common names, you may list multiple names here.

For siRNA submissions . . .

The "anti-sense" strand is the siRNA strand that is complementary to the target mRNA and that will be binding to the mRNA.

Sense sequence (5'-3')
Provide the "sense" sequence of the siRNA including overhangs.

Sense sequence position
Provide the position of the sense nucleotides present in the sense strand (not including overhangs). The format should be "0:18", where "0" is counted as the first nucleotide position on the strand.

Sense overhang position
Provide the position of the the overhang in the "sense" strand (format 19:20).

Anti-sense sequence (5'-3')
Provide the "anti-sense" strand sequence of the siRNA (i.e. the strand that binds to the mRNA).

Anti-sense sequence position
Provide the position of the sense nucleotides present in the sense strand (not including overhangs). The format should be "0:18", where "0" is counted as the first nucleotide position on the strand.

Antisense overhang position
Provide the position of the the overhang in the "anti-sense" strand (format 19:20).

For shRNA submissions. . .

The "anti-sense" strand section of the shRNA strand that is complementary to the target mRNA and that will be binding to the mRNA once the shRNA is cleaved.

Full sequence (5'-3')
Provide the sequence of the cloned oligonucleotide in the following format:
[end with cloning site]-sense-loop-antisense-[TTTTT]-[end with cloning site].
Please note that sections of sequence in brackets are not required, but may be useful to other researchers.

Sense sequence position
Please provide the nucleotide position of the "sense" sequence within the shRNA (format "7:25", where the first nucleotide position is treated as "0").

Anti-sense sequence position
Please provide the nucleotide position of the "anti-sense" sequence within the shRNA (format "36:54", where the first nucleotide position is treated as "0")

Target sequence
Provide the target sequence of the mRNA at the siRNA binding site.

Comments
Please provide any further information regarding the siRNA design that would be useful.

Results
In order for a sequence to be included in the MIT/ICBP siRNA Database, it must be validated through measurement of either mRNA or protein knockdown.

Experiment name
The NCBI Probes Database requires that all submitted results have an experimental title. Please provide a basic, one line, description of your experiment.

If you are submitting more than one siRNA against the same gene and tested the siRNAs together, use the same name for each submission.

Organism
The species from which the gene being knocked down originated.

Experiment subject
Ex. cell culture

Cell type
Ex. T lymphocyte, fibrocyte

Cell line
Name of cell line (or "primary cell ")

Gene of origin
Is the target mRNA in your experiment an endogenous target or a transfected gene target?

Treatment prior to RNAi
Did the target cells undergo special treatment conditions prior to use of siRNAs?

Vector
The vector used to deliver the siRNA to the cell.

Dose
The dose of the siRNA used.

Delivery method
Method used to deliver the siRNA to the target cell.

mRNA suppression
Provide the percent mRNA knockdown achieved in your experiment.

Method of mRNA detection
List the method used to detect the mRNA knockdown (ex. real-time PCR, Northern blotting)

Protein suppression
Provide the percent mRNA knockdown achieved in your experiment.

Method of protein detection
List the method used to detect the protein knockdown (ex. Western blot , luciferase assay)

Phenotype observed
Did the administration of your siRNA result in an observable phenotype? If yes, please describe.

Notes
Please provide additional information regarding your experimental setup and/or results that will assist other researchers in assessing your siRNA vector.

How do I search for a gene of interest?

Each siRNA submitted to our database has its own individual page containing information on the siRNA construct and experimental validation. Our search feature will allow you to search for any content within these pages to find potential siRNAs of interest.

Please not that it takes our search engine several days to pick up new additions to the website. If you do not see your sequence of interest using the search page, you may find it by browsing the results tables.