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PacBio Sample Submission Form

Offering PacBio services on the newest PacBio Sequel II as of June 2019, all Sequel I systems have been retired. The Sequel II system produces 8-10x the data amount for ~2X the cost of the Sequel I with the same quality profile.

We can take samples/libraries from any stage and carry them through to sequencing. We offer High Molecular Weight Extractions, PCI cleans for user provided gDNA, shearing, BluePippin and ELF size selection, low input library preps, HiFi (12kb ccs) Library preps, Long Insert library preps up to 100kb, and 8M SMRTcell processing. We can demultiplex, generate ccs reads, and run the PacBio IsoSeq pipeline. Further analyses cannot be accommodated in house and will be outsourced to UC Davis.

HiFi/DNA – Please submit at least 5 ug of DNA eluted in 50 uL of EDTA free buffer per SMRT cell. We can work with a little as 100 ng, however we will need to amplify your DNA and there will be an upcharge for using the low or ultra low input kits. Please get in touch with us if you will be submitting less than 3 ug of DNA. The modal sizing of your DNA should be greater than 40k bp, the 260/280 ratio should be between 1.8-2.0, and 260/230 ratio should be greater than 2.0. If you cannot provide sizing information prior to submitting, we can run sizing for you at an additional cost.

Amplicons – The input amount needed is dependent on the size of your amplicon. Please refer to the chart below. We recommend erring on the side of more material as we see a decent amount of loss during the library prep process.

Amplicon Size Input DNA Amounts per Pool (ng)
250-500 bp 250 – 500*
500-1000 bp 250 – 500*
1-3 kb 500 – 1000
3-10 kb 1000 – 2000
15 kb 1500 – 3000

 

IsoSeq/RNA – Please submit RNA samples with a minimum concentration of 45 ng/uL. The library prep process requires 300 ng of RNA in 7 uL. RNA should have a RIN score of 7 or higher, 8 or higher preferred. If you cannot provide sizing and a RIN score prior to submitting we can run this for you at an additional cost.

Prepped libraries – Please contact us at gsl-fgl@berkeley.edu to determine how much of the library we will need.

Tissue – Please contact us at gsl-fgl@berkeley.edu before submitting tissue samples.

 

Please email the GSL for any other inquiries (gsl-fgl@berkeley.edu).