The links on this page do not yet work.

Before you submit a sample

The final library PCR should require only 15 or fewer cycles to generate a quantity of library material that can be gel-purified. In most cases, if you require more than 15 cycles, you should start over and optimize the previous steps of your experiment, because a larger number of cycles indicates that you had too little library for adequate representation, resulting in a bottlenecked sample. For more information, talk to experienced library builders or contact us.

If you are new to experiments that have sequencing as the assay endpoint, start with a couple of test samples before you begin work on your precious experiments.

Do not assume that an experiment that has sequencing as the assay endpoint is the same as an experiment that has array detection or qPCR as the assay endpoint. There are important differences in protocols.

To get a feel for these types of experiments, read one or more of the protocols listed on the right.

Protocols

These protocols are in routine use in the Sidow lab. Please use at your own risk and contact us if you need advice. If you would like to provide a protocol for experiments not listed here please contact us.

ChIP-seq

3SEQ

Genomic DNA for whole genome sequencing

submission Requirements

Do you know your ABQ? We require BOTH Bioanalyzer (B) and Qubit quantification (Q). We do not accept nanodrop or any other type of quantification. The PAN facility has fast turnaround for Bioanalyzer; Sidowlab has a Qubit reader, but you need to buy the supplies. We also require an Account (PTA) number. We will not accept your samples without ABQ.

"A" is obvious, but why do we require "BQ"? Because accurate quantification is essential for optimal numbers of reads and we've learned over the years that the combination of B and Q is best. If you have substantially different results from B vs Q your library prep may be compromised and you may not get the results you were hoping for. Here is an example of a few good Bioanalyzer results.

Library concentration should be at least 5 ng / µl; higher is better. Under exceptional circumstances we may accept a sample of lower concentration. Please don't do funky stuff like lyophilizing the sample to get the concentration up. Your gel purification should give enough material to get to 5 ng / µl.

How to submit a sample

Did you read the "Requirements" section? Thanks!

1. Download the submission spreadsheet here and fill out the information.

2. Email the submission spreadsheet and the bioanalyzer results to zweng@stanford.edu

3. Come to R301 (see Contact tab above) to drop off the samples and say hello.