Payment

Invoices will be submitted to users by Harvard's Accounts Receivable department at the conclusion of library construction. Payment should be made to the address on the invoice you recieve from Accounts Receivable:

Harvard University
Accounts Receivable
1033 Massachusetts Ave.
2nd Floor
Cambridge, MA 02138

We accept Harvard 33-digit billing codes (required for internal users) and purchase orders. POs should be made out to the Harvard Accounts Receivable address above.  For groups with multiple affiliations (e.g. your institution and HHMI) please let us know at the time of ordering which affiliation you intend to use as this may affect your pricing.  The core requests payment within 30 days of the invoice.

Sample Biosafety

The Nascent Transcriptomics Core is a BSL-2 facility and is authorized under our COMS registration for work with materials in these classifications:

• Biosafety Level 1 (BSL1) for laboratory use of synthetic oligos, transgenic-mouse-derived tissues/cells, mouse cell lines, insect cell lines, Saccharomyces cerevisiae, and Schizosaccharomyces pombe
• Biosafety Level 2 (BSL2) for laboratory use of patient-derived cells/tissues and established human cell lines (stably genetically modified)

Biological agents requiring measures greater than BSL-2 may not be submitted without prior arrangement made well in advance of sample submission. Our goal is to enable our users to perform the experiments necessary to advance their research but we reserve the right to decline projects on the basis of potential biosaftey risk.

Users must disclose the types of biological materials submitted to the core, including biosafety level and any special handling requirements.

By submitting samples to the core, users affirm that the materials are BSL-2 or less and do not contain infectious viral particles (e.g. SARS-CoV-2, packaged lentiviral vectors) or express restricted, toxic proteins (e.g. botulinum toxin). Users also affirm that, to the best of their knowledge, their experiment is covered under their own COMS registration or is compatible with the core's COMS registration (i.e. consistent with BSL-2 guidelines summarized above).

Data distribution and analysis

The cost of all projects includes a fee for data QC analysis and staff time handling and transferring your data. Thus, this fee cannot be waived even if you opt to perform your own data analysis.

Data analysis only available for samples sequenced under the supervision of our core or connected with such samples (e.g. users' RNAseq data analyzed in parallel with PRO-seq generated by the core). If you opt to perform your own deep sequencing of libraries we build, we may be unable to assist with data analysis. Please note that PRO-seq libraries have short read lengths which our partner sequencing cores are familiar with clustering at good efficiency. If you opt to do your own sequencing, inefficient clustering may result if your chosen sequencing facility is unfamiliar with clustering short reads libraries. NTC cannot take responsibility for low read depth resulting from user sequenced libraries.

Raw sequencing data from your project will be made available for download after we receive it. Please download your data promptly and verify that it is complete. The core cannot guarantee that raw data will be preserved longer than 30 days after it is made available to you. An exception is made for projects where the core is involved in data analysis. In this case, data will be preserved until the agreed analyses are completed. After analysis is complete, processed results will be made available for download and you will have 30 days to confirm transfer.  Data older than the date of raw sequencing availability plus 30 days or of data analysis completion plus 30 days, whichever is later, may be deleted without notice.

Reasonable Efforts

If samples fail QC during construction you will be notified and we will discuss how to proceed.

1. Failed Libraries:
   1. If samples fail but our controls are successful, you will be responsible for reagent and labor costs of library construction.
   2. If samples fail for reasons we determine are our responsibility we will make one attempt to reconstruct them at no additional cost to you.
2. Failed sequencing

We do not perform sequencing ourselves and cannot discount sequencing or offer free sequencing runs. Users are responsible for all sequencing costs regardless of outcome.

1. If a sequencing run fails we will work with our sequencing core partners to resolve the issue on your behalf. Since this aspect of the project is outside of our direct control, we are subject to the policies of our partner cores.
2. If a sequencing run is technically good but your data quality is poor, you will still be responsible for all labor, reagent, sequencing, and analysis costs up to that point. If it is necessary to reconstruct these libraries, they will be charged at the standard rate.

Method Specific Policies

PRO-seq
Permeabilized cells submitted for PRO-seq will be counted and assessed for quality. If the cells are of insufficient quality or quantity we will not start library construction and will discuss with you how to proceed. There is no charge for failed cell QC but replacement samples may go to the back of the queue. To avoid possible delays, please take care with your permeabilized cell preps.

The core uses 1 million permeabilized cells for each PRO-seq library. It is possible to construct libraries with fewer cells but we cannot guarantee success with low input libraries. Users requesting low input library construction will be charged regardless of whether these libraries succeed or fail.

TT-seq
Users are responsible for labeling and accurate counting of their cells and, when submitting total RNA, for the quality of their RNA. We will notify you if RNA quality--RIN > 8--is sufficient for library construction. Low quality RNA is unsuitable for library construction and we may require additional material to proceed.

Acknowledgement of Services

In order to satisfy institutional reporting requirements and to support ongoing operations of the core, NTC requests that users acknowledge work performed by NTC in peer-reviewed publications in one of these ways:

• in the acknowledgements section:
The authors would like to thank the Nascent Transcriptomics Core at Harvard Medical School, Boston, MA for performing [PRO-seq / TT-seq] library construction and for assistance with data analysis.

• in the methods section:
[PRO-seq / TT-seq] library construction and data analysis was performed by the Nascent Transcriptomics Core at Harvard Medical School, Boston, MA.

NTC is happy to provide draft methods text describing the services performed by the core. Please notify us of publications using data generated by the core so we can add your papers to our bibliography.  Doing so helps ensure that we can continue to offer our services to the research community and is greatly appreciated.

Though we never insist upon it, in cases where NTC staff go above and beyond our standard services to subtantively advance our users' research goals, it may be appropriate to discuss authorship credit for the core staff involved in the project.