Genomic Sample Services Facility

 ******************PLEASE NOTE******************
Samples Services has relocated to 300 Longwood Enders Research Building, 2nd floor, room EN 284.

 Sample submission directions have been updated below along with our delivery addresses.

Why is Sample Services moving?
This move reflects a change in management – Sample Services will no longer be supported by the Molecular Genetics Core Facility (MGCF).  Instead it will become part of the new institutional Biorepository – BCH Biobank Core, led by Executive Director, Wendy Wolf, PhD.

Who do I contact regarding my samples and services?
You may continue to email samples@iddrc.org to reach the following staff members who will also transition over to BCH Biobank Core:

Tram Anh Tran – Manager, Biorepository Operations
Kyle Gowen – Research Assistant
Christopher Liu – Research Assistant

How will this affect me?
For now, this should have little impact – you will need to go to Enders EN 284 to submit and pick up samples.  And your monthly invoices beginning in December (for work completed in November) will come from BCH Biobank Core.  Otherwise everything will remain the same.

In the upcoming weeks, you will receive additional information about BCH Biobank Core and changes that may impact you to help you decide whether you would like to continue working with us.

Will the same services be offered?
Yes.  Additionally we anticipate major improvements in our services and turnaround times as BCH Biobank Core has obtained new equipment/automation to improve capacity and throughput.  More information will provided as changes are implemented.

Will there be a change in service fees?
Our service fees will remain as is until January 2013. After January, there will be an update to our service fees which have always been subject to change and generally evaluated on an annual basis to ensure that our costs are covered.

Do you have a new website?
Our new website is currently under construction.  You may continue to visit this site.

Description:

The Genomic Samples Services Facility functions as a core service designed to manage samples for genomic projects by offering the processing and banking of biological specimens. Funded mainly by The Manton Center for Orphan Disease Research at Children’s Hospital Boston, this core service is also open to other research investigators in need of project sample management.

Upon arrival, specimens are entered into our Laboratory Information Management System (LIMS) and assigned unique bar-code IDs. The Core uses Progeny LIMS for all sample tracking and inventory management. A detailed account of the specimen history including processing history, extraction information, quantity records, results quality, and storage location is maintained for each and every specimen and any subsequent aliquots. Standard procedures include DNA extraction, RNA extraction, and long-term storage at -80C.

Services:

The Genomic Sample Services Facility currently performs DNA extraction from both blood and saliva collected in Oragene DNA kits. Most DNA extractions are automated on the AutoPure LS instrument with Gentra Puregene reagents, a modified salting-out precipitation method that produces high molecular-weight, archive-quality DNA.  Manual extractions may be performed for samples where quantity or quality is not optimal.

DNA extraction service includes a comprehensive QC with Nanodrop and Quant-iT, preparation of aliquots, and 1 year of freezer storage.  Quant-iT™ is highly selective quantitation assay for double-stranded DNA unlike absorbance at 260nm which may reflect the presence of RNA and other contaminants, while aliquots minimize freeze thaw cycles and may help prevent sample loss by limiting contamination and allowing for storage in multiple locations.

RNA extraction in the MGCF is performed using the PAXgene Blood RNA system. The PAXgene tubes contain an RNA stabilizer that allows the blood to be stored without RNA degradation. Customers provide the Core with their collected PAXgene blood RNA Tube and the Core performs the extractions on the QIAcube instrument using the PAXgene Blood RNA Kit, which utilizes a silica-membrane-based spin-column technology.  Additionally each RNA sample is assessed for quantity and quality on our Nanodrop and Agilent Bioanalyzer instruments, respectively.

The Core will also prepare samples for downstream applications in single tube(s) or 96-well plate formats.  Samples may be picked up from our facility or we can ship via FedEx.

Instruments:

Agilent 2100 Bioanalyzer

NanoDrop 8000

PerkinElmer Victor3 1420 Multilabel Plate Reader

Qiagen AutoPure LS

Qiagen QIAcube

Submitting Samples:

To begin a project in the Genomic Sample Services Facility, you must complete a one-time User Registration Form and a Submission Request Form per protocol or project.  Please email your completed forms to samples@iddrc.org for approval, after which you may submit samples.

All sample submissions must be clearly labeled with a unique subject identifier and accompanied with a collection form itemizing each sample per subject with collection date and time. You may use our general Sample Submission Form or provide your own form with similar information.

Handling Instructions:
Oragene® DNA collection kits (http://www.dnagenotek.com) may be stored and submitted at room temperature. Please follow the Oragene mailing guidelines for proper packaging instructions for shipment.

Blood for DNA should be collected in an EDTA (Lavender top) vacutainer and stored as follows prior to submission (in order of preference):

1) < 24 hours @ 4C
2) < 24 hours @ Room temperature (RT)
3) < 72 hours @ 4C
4) < 6 months @ -80C (Freeze immediately after collection)
5) < 6 months @ -20C (Freeze immediately after collection)

There is a refrigerator for RT and 4C Blood for DNA submissions and a freezer for already-frozen submissions.

PAXgene™ RNA blood should be collected in a PAXgene™ Blood RNA tube and submitted at room temperature within 24 hours of collection. Alternatively, if you are unable to submit within 24 hours of collection, you may submit frozen on dry ice. Please note you MUST follow the PAXgene™ Blood RNA System instructions very closely prior to freezing the sample. It is highly recommended that you review both the Collecting Specimens in PAXgene Blood RNA Tubes Video and Freezing Specimens in PAXgene Blood RNA Tubes Video. PAXgene™ RNA bloods that are submitted at room temperature will be frozen 24 hours from collection at -80C. RNA purification is performed monthly in batches of up to 12 with a standard 2-hour thaw.  If you require a different thaw protocol, please let us know.

DNA analysis with dsDNA-specific quantitation, Quant-iT should be prepared in strip tubes or 96-well plates. Please prepare 5ul aliquots and submit frozen. If you also require gel electrophoresis, then include 10ul.  Complete and include our DNA Analysis Form with your submission. You must specify High Sensitivity or Broad Range assay. Our recommendation, based on Nanodrop readings, is as follows:

Source High Sensitivity Broad Range
Blood 0-100 ng/ul 100-1000 ng/ul
Oragene DNA 0-250 ng/ul 250-1000 ng/ul

i.e., if source is blood and your anticipated concentration range is 0-100 ng/ul, then select High Sensitivity.

Please do not mix samples for both assays. Samples may share the same plate but should be segregated. All samples are run in duplicate. You will receive concentration (ng/ul), %CV, and standard deviation results for each sample. We suggest that you resubmit samples with %CV >15 as data may not be accurate.

Delivery Instructions:
All submissions must include a document itemizing each sample with basic collection information. You may use our general Sample Submission Form or provide your own. We also request that you email samples@iddrc.org with delivery notification and the shipment tracking number, if applicable, 24 hours prior to arrival. We will email you if we do NOT receive your shipment or there is any problem(s) with your submission.

Personal delivery or courier service – Monday through Thursday, 9-5PM and Friday 9-3PM, except holidays.

Genomic Sample Services
c/o Tram Tran
Boston Children’s Hospital
300 Longwood Ave,
Enders Research Building 284
Boston, MA 02115
(617) 919-7050 Laboratory
(617) 919-3384 Office

Take elevators to 2nd floor, the BioRepository is toward the front of the building in the northern corner.

FedEx, UPS, or USPS packages – Send Priority Overnight Monday through Wednesday.

Do NOT ship Thursday, Friday, or before a Holiday.

Tram Tran
Boston Children’s Hospital
61 Binny Street
EN 284
Boston, MA 02115
(617) 919-7050 Laboratory
(617) 919-3384 Office

Please email samples@iddrc.org with delivery notification and the shipment tracking number, if applicable, 24 hours prior to arrival. We will email you upon receipt.

Please note that if samples are not submitted as outlined above, we cannot guarantee normal yields and quality. Also any specimen handling and delivery to the laboratory is expected to be in compliance with rules and regulations of Department of Transportation (DOT) and International Air Transport Association (IATA) – all personnel preparing or handling shipments must have received training and certification within the past 2 years.

Requesting Sample send-outs:

To request samples from the Genomic Sample Services Facility, you must complete our Sample Send Out Request Form and email to samples@iddrc.org. You will receive a confirmation email with pick up information. Samples will be frozen unless otherwise specified and may be picked up from our facility or our staff can send via FedEx. Please allow at least 1 week for us to complete your request. Also note, if you are sending samples for whole-genome sequencing to CGI or exome sequencing to Axeq, please consult our Next-Gen Sequencing Facility page.


Pricing

Service Expected Turnaround  Fee per sample
DNA extraction from 1-5ml blood* 2 weeks $35.00
DNA extraction from 5-10ml blood or Oragene DNA* 2 weeks $40.00
DNA analysis with dsDNA-specific quantitation, Quant-iT 1 week $2.00
DNA analysis with Quant-iT and gel electrophoresis 1 week $5.00
DNA prep, single tube to 96-well plate 2 weeks per plate $200.00
DNA prep, 96-well plate to 96-well plate 1 week $20.00
RNA extraction from PAXgene RNA blood** 1 month $35.00
RNA analysis with Agilent Bioanalyzer   Offered through Microarray Core
(-80C) Freezer storage for 1 year***   $1.00
Sample send-out, includes required aliquot/dilution prep 1 week $2.00
FedEx Shipment includes 1 insulated shipper and dry ice****   $50.00
 
* Includes QC with Nanodrop and Quant-iT, aliquot prep, and 1 year of freezer storage or return to PI.
** Includes QC with Nanodrop and Agilent Bioanalyzer.
*** Assumes standard 1.8-2.0ml cryovial tube.  For non-standard tubes, email tram.tran@childrens.harvard.edu for approval and custom price.
****plus FedEx charges or you may provide FedEx account no.
 
For any other service requests, email tram.tran@childrens.harvard.edu for approval and custom price quote

 

Contact Us

Sample Services Team [samples@iddrc.org]

(617) 919-7050

Or Individual members

Kyle Gowen

Chris Liu

Tram Tran

Files For Download