Sample Submission Guideline

​

Fill out the Sample Submission Form excel sheet:
Make sure that upon labeling your samples, the name on the excel sheet matches the name printed on the vial of your sample. Send completed sheet along with the samples during shipment.

Download the Sample Submission Form

Prepare samples:
For each sample, prepare a vial of 6-10 x 10⁶ drug-treated or vehicle-treated cells (~70-80% confluency at time of collection), collected right after drug treatment in 1 mL of complete media + 10% DMSO into cryovials and frozen to -80°C with isopropyl alcohol. Treatment of cells with a pan-caspase inhibitor is suggested alongside of drug treatment if there is a significant apoptotic cell fraction. Submission of biological replicate samples of each condition and of vehicle-treated negative controls are highly recommended.

If customers choose to follow up on their own with NGS or qRT-PCR on processed samples, BreakSight will return to customers a 1.5 mL Eppendorf tube of purified DNA break fragments in 50 µL TE buffer (retrieval) and a 1.5 mL Eppendorf tube of genomic DNA in 100 µL TE buffer (input) that are generated from the performance of our assay. Turnaround time is 5-7 business days after receipt of samples per 1-12 sample batch.

Sonication to an appropriate fragment size and preparation into libraries of retrieval and input samples are necessary prior to NGS.

Send samples:

Please ship samples overnight on dry ice to:

BreakSight, Inc
ATTN: Nishita Shastri
7540 Windsor Drive
Suite 210
Allentown, PA 18106

Include printed excel sheet listing samples and services requested. Email tracking number of shipment to nishita.shastri@breaksight.net at the time of shipment.

*Samples may only be shipped Mon-Wed for overnight delivery to be received no later than 1pm EST the following day.

If NGS is requested on samples (DDsite):

BreakSight will ship customer’s processed samples (retrievals and inputs will henceforth be considered as separate samples) to an NGS provider directly from our facilities. The NGS provider will perform sample QCs, sonication, library preparation, library QCs, and 150 bp paired-end sequencing to generate 60 million read-pairs per sample. Turnaround time is up to 5 weeks.

If Bioinformatics is requested (DDinsight and/or DDinsight⁺):

BreakSight will perform bioinformatics analysis on customer’s NGS-generated FASTQ files to call statistically significant peaks for each sample and condition. Data files that include quality checks and analysis results will be sent to customers.

For best interpretive results on peak-calling, retrieval and input FASTQ data from two biological replicates per condition are recommended, including from two biological replicates of vehicle-treated samples (negative control).