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Equipment and Technology: A. Bionano Genomics Chromosomal Mapping Instrument (Saphyr)
Kathryn Sheldon, Ph.D. | |
James Broach, Ph.D. | Director of the Institute for Personalized Medicine |
Hours | Location |
Monday-Friday/ 9am - 5pm By Appointment |
500 University Drive College of Medicine, C2706 Hershey, PA, 17033 |
Name | Role | Phone | Location | |
---|---|---|---|---|
IPM-Research |
Service list |
► RNA Isolation (1) | |||
Name | Description | Price | |
---|---|---|---|
Quick-cf RNA Serum & Plasma Kit extraction |
Placeholder until I get more information on the kit and the additives I need to include in the pricing. |
Inquire | |
► DNA Isolation Menu (4) | |||
Name | Description | Price | |
DNA Clean & Concentrator-25 |
Zymo Research DNA Clean & Concentrator-25. Utilize for DNA concentration and/or buffer change required for downstream enzymatic processes. Allows for RNase A treatment of DNA samples, using column based purification to remove enzyme. For DNAs between 50 bp-23 Kb. |
Inquire | |
DNeasy Blood & Tissue Kit |
For purification of total DNA from animal blood, animal tissue, rodent tails, ear punches, cultured cells, fixed tissue, bacteria, insects |
Inquire | |
genomic DNA Clean & Concentrator-25 |
Zymo Research genomic DNA Clean & Concentrator-25 Utilize for gDNA concentration and/or buffer change required for downstream enzymatic processes. Allos for RNase A treatment of DNA samples, using column based purification to remove enzyme. For DNAs between 50 bp-200 Kb. |
Inquire | |
Quick-cfDNA Serum & Plasma Kit |
Cell-free and nuclear DNA isolation of ≥100 bp fragments. Validated sample types include serum, plasma, amniotic fluid, and saliva. |
Inquire | |
► DNA Evaluation (6) | |||
Name | Description | Price | |
PicoGreen dsDNA Assay |
Invitrogen QuantiT PicoGreen dsDNA Assay Kit, Quantity: 1mL kit, Assay: dsDNA Quantitation, Quantitation Price per ml is listed. |
Inquire | |
Qubit BR dsDNA Assay |
Measure dsDNA concentration using fluorometric reagent and assay tube. |
Inquire | |
Qubit HS dsDNA Assay |
Measure dsDNA concentration using fluorometric reagent and assay tube. |
Inquire | |
qPCR plate and film |
Cost of 384-well qPCR plate. Necessary for qPCR runs. |
Inquire | |
SYBR Green qPCR Test |
Price per well; for a DNA sample, dilution or replicate. Quantitect Sybr Green, 2x; 384 well plate, 10 ul reactions. DNA oligos, plate and film, QuantStudio 12K flex, are not included. |
Inquire | |
RNase P DNA Detection Agent |
Price per DNA sample and DNA dilution. RNase P TaqMan Detection Kit quantifies a single copy gene by comparison to human DNA standards. Cost is listed for the price per well. Total wells used is calculated by the number of standards, DNA samples and dilutions tested, and replicate values. Recommended testing for amplifiable DNA is performed in triplicate for 7 human DNA standards, 1 NTC, and 2 DNA dilutions. RNase P DNA Quantification is performned in Batch: Cost of PCR plate and film (IPM) Cost of RNase P Detection Reagent (IPM) Cost of TaqMan Expression Master Mix (GS) Cost to run a plate in Genome Sciences (GS)
|
Inquire | |
► DNA Library Preparation (4) | |||
Name | Description | Price | |
AmpliSeq for Illumina BRCA Panel Library |
Reagent cost per DNA sample. AmpliSeq library preparation for illumina using the BRCA Panel for somatic and germline mutation detection. Amplification based target enrichment. |
Inquire | |
Lab supply charge - AmpliSeq for Illumina BRCA Library Batch |
Charge necessary for AmpliSeq for Illumina BRCA Library batching, per batch of ≤48 DNAs. AmpliSeq library preparation for Illumina using the BRCA Panel for somatic and germline mutations in BRCA1 and BRCA2. Amplification based target enrichment. |
Inquire | |
AmpliSeq for Illumina Cancer HotSpot Panel v2 Library |
Reagent cost per DNA sample. AmpliSeq library preparation for Illumina using the Cancer Hotspot Panel v2. Amplification based target enrichment. |
Inquire | |
Lab supply charge - AmpliSeq for Illumina Cancer HotSpot Panel v2 Library Batch |
Charge necessary for AmpliSeq Cancer HotSpot Panel v2 batching, per batch of ≤96 DNAs. AmpliSeq library preparation for Illumina using the Cancer Hotspot Panel v2. Amplification based target enrichment. |
Inquire | |
► Misc Genome Sciences Core Requests (6) | |||
Name | Description | Price | |
DNA/RNA QC |
Placeholder for necessary Genome Sciences service request necessary for IPM collaborative research. Sizing and quantitation accuracy of the results is dependent on choosing correct chip. Please see ranges below. If your sample is not in the QC range of the selected chip, we are not responsible. If we run an additional chip, you will be charged again. If you have less than 12 samples but need results quickly, you will be charged for the entire chip. Partial charges are only possible when we have enough samples to fill an entire chip.
|
Inquire | |
DNA/RNA QC - High Sensitivity |
Placeholder for necessary Genome Sciences service request necessary for IPM collaborative research. Sizing and quantitation accuracy of the results is dependent on choosing correct chip. Please see ranges below. If your sample is not in the QC range of the selected chip, we are not responsible. If we run an additional chip, you will be charged again. If you have less than 11 samples but need results quickly, you will be charged for the entire chip. Partial charges are only possible when we have enough samples to fill an entire chip.
|
Inquire | |
MiSeq Reagent Kit v2 (300) |
12-15 mil Single Reads. Placeholder for necessary Genome Sciences service request necessary for IPM collaborative research.
|
Inquire | |
MiSeq Reagent Micro Kit, v2 (300 cycles) |
4 million reads. |
Inquire | |
MiSeq Reagent Micro Kit, v2 (300 cycles) |
4 million reads. |
Inquire | |
MiSeq Reagent Nano Kit, v2 (300 cycles) |
1 million reads. |
Inquire | |
► Structural Genomics (12) | |||
Name | Description | Price | |
Eve Cell Counting |
NanoEnTek's Eve cell counting slides. Two chambers available per slide. |
Inquire | |
Countess slides used |
Thermo Fisher Scientific's Countess cell counting chambers. Two chambers available per slide. |
Inquire | |
Hemocue microcuvette |
For White Blood Cell counts. |
Inquire | |
Bionano Prep SP DNA Isolation Kit |
Select this item to reimburse the IPM for the cost of reagents. Includes Bionano Prep SP BMA, Blood and Cell, or Tissue DNAIsolation Kits. |
Inquire | |
SP Bone Marrow Aspirate DNA Isolation Kit - Prepurchased |
Please select this item for the ALL project in collaboration with Drs. Broach and Dovat. Kitted reagent part of 30 genome bundle purchased for this specific project. Bundle purchased on PO 802560.
|
Inquire | |
TissueRuptor Disposable Probes - Prepurchased |
Dr. Goldenberg prepurchased this item and it is not for use by anyone other than his research fellows. Thank you. |
Inquire | |
Qubit BR dsDNA Assay |
Measure dsDNA concentration using fluorometric reagent and assay tube. |
Inquire | |
Direct Label and Stain (DLS) Kit |
Select this item to reimburse the IPM for the cost of reagents. |
Inquire | |
Direct Label and Stain (DLS) Kit - Prepurchased |
Please select this item for the ALL project in collaboration with Drs. Broach and Dovat. Kitted reagent part of 30 genome bundle purchased for this specific project. Bundle purchased on PO 802560.
|
Inquire | |
Qubit HS dsDNA Assay |
Measure dsDNA concentration using fluorometric reagent and assay tube. |
Inquire | |
Saphyr Optical Mapping - 1 FC |
Select this item to reimburse the IPM for the cost of reagents. Three samples must be processed on one Saphyr chip as there are 3 flow cells within. |
Inquire | |
Saphyr Optical Mapping - Prepurchased |
Please select this item for the ALL project in collaboration with Drs. Broach and Dovat. Kitted reagent part of 30 genome bundle purchased for this specific project. Bundle purchased on PO 802560.
|
Inquire | |
► PCR Anchored Library (5) | |||
Name | Description | Price | |
Phusion Hot Start II enzyme |
Enter volume of Phusion Hot Start II enzyme used in PCR Anchored Library prep reaction in ul. Phusion II HIgh Fidelity HotStart Thermo Fisher Scientific F549S 50 units/50 ul |
Inquire | |
10 mM dNTP |
Enter volume of 10 mM dNTP used in PCR Anchored Library prep reaction in ul. |
Inquire | |
sparQ SPRI |
Enter volume of sparQ SPRI used in ul. QuantaBio 95196-060 60ml/VWR 76302-832 |
Inquire | |
100% EtOH |
Enter volume of 100% Ethanol used for sparQ SPRI washes in ml. Ethyl Alcohol, 200 proof Price per ml |
Inquire | |
Water, nuclease-free |
Enter volume of nuclease free water used for sparQ SPRI washes here in ml. |
Inquire | |
► Covaris E220 (3) | |||
Name | Description | Price | |
Crimp Cap | Inquire | ||
milliTUBE | Inquire | ||
Snap Cap | Inquire | ||
► unclassified (2) | |||
Name | Description | Price | |
Saphyr Optical Mapping - Prepurchased |
Please select this item for the ALL project in collaboration with Drs. Broach and Dovat. Kitted reagent part of 30 genome bundle purchased for this specific project. Bundle purchased on PO 802560.
|
Inquire | |
sparQ SPRI |
volume of sparQ SPRI used. |
Inquire |