NGS Sample Prep


The core prepares libraries that are suitable for sequencing on Illumina sequencers. Library preparation includes Bioanalyzer and MiSeq quality control, normalization, pooling, and sample submission to UCSF sequencing cores. We offer several standard protocols for sample preparation. 


Universal Plus mRNA [Tecan]: this method generates strand-specific libraries covering protein coding RNAs (mRNAs) and other long polyadenylated transcripts. This method requires 10ng-1µg total RNA starting material and a polyA selection step is included in the method. 

SMART-seq v4 [Takara Bio] + Nextera Flex [illumina]: these methods are appropriate when less RNA is available for analysis, generating strand-specific libraries covering protein coding RNAs from 1-1000 cells or 10pg-10ng of RNA.

Universal Plus mRNA [Tecan] + FastSelect ribo/globin Depletion [QIAgen]: these methods generate strand-specific libraries covering both polyadenylated and non-polyadenylated long transcripts. Requires 50ng-1µg total RNA and a ribosomal depletion step is used to remove rRNAs, which would otherwise dominate the libraries. We also offer a version of this method that includes globin depletion and is useful for blood samples.

Ovation RNA-Seq v2 [Tecan] + NexteraXT [illumina]: these methods are appropriate when less RNA is available for analysis, and can be used with as little as 500 pg total RNA.


NexteraXT [illumina]: this method can start with as little as 1ng of chromatin immuno-precipitated DNA (supplied by the user).

Small RNA-Seq

Modified TruSeq Small RNA [Illumina]: this method is designed to sequence miRNAs but also captures some other small RNAs and fragments of larger RNAs. We use random-end adapters to minimize ligation bias and optimized the method to work with as little as 10ng of total RNA.