HT Sequencing Core is a full-service NGS facility providing instrumentation, library preparation, and sequencing services to CHOP, UPenn, and to some extent to external investigators. Whether you want to sequence libraries that you generated yourself, or assistance with library preparation, we can help. Our goal is to enable in-house high throughput sequencing service and to make the HTS Core accessible to everyone interested in sequencing projects.
HT Sequencing Core has capabilities ranging from highly focused analysis of miRNA to whole genome, epigenome, exome, and transcriptome sequencing. Services are available for a diversity of study designs; starting with as few as 12 samples to large projects involving hundreds of samples, we are working with investigators to provide optimized protocols for each study. We understand that not all research is alike, we offer consulting services for custom experiments tailored to your research needs. We are here to listen and create solutions.
For any sequencing project, except self-servce, please request a project ID. Samples can be submitted only after the requested service has been aproved in iLab and a project ID has been issued. For sample drop off please contact us through email, sample dropoff M-F: 9-12AM and 1-4PM.
Turnaround Time (TAT) varies based on the complexity and volume of projects, TAT for sequencing your own libraries is max 14 days from the date of sample drop off, NGS for small projects that include libary prep and sequencing take up to 4 weeks, for large projects which include libary prep and sequencing of more than 50 samples expect a TAT of 6 weeks or more, TAT is calculated from the date of sample submission. Inquires "have you sequenced my samples/pool?" are not going to be answered.
Our services
To Reserve a qPCR instrument please select the "Schedule/Reserve your Instrument" tab, for everything else else please select the "Request Service" tab.
Please Note: External academic (Non CHOP/UPENN) researchers should add 10% to posted rate. External commercial customers should add 30% to posted rates. These charges will appear on the final invoice.
Teodora Orendovici | Technical Director
Hours | Location |
Monday - Friday 8:00 AM - 5:00 PM |
A450 Colket Translational Research Building, 3501 Civic Center Boulevard, Philadelphia, PA, 19104 |
Name | Role | Phone | Location | |
---|---|---|---|---|
Teodora Orendovici |
Technical Director
|
814-574-1631
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orendovict@chop.edu
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CTRB A340B
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Stephen Mahoney |
Research Associate
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215-896-6027
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mahoney@chop.edu
|
CTRB A450D
|
CHOP HTS Core |
General Inquiry
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267-425-5866
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HTSCore@chop.edu
|
CTRB A450D
|
Ashley Bushey |
Research Technician
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215-896-6027
|
busheya@chop.edu
|
CTRB A450D
|
Service list |
► BeadBug Homogenizer (1) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
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BeadBug homogenizer self-service |
The BeadBug homogenizer can simultaneously process up to six samples in 2.0ml tubes. It is available free of charge with your own tubes and beads. |
Inquire | ||||||||||||||||||||||||||
► Library Preparation Services (12) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
ATAC-seq Library Prep |
Assay for Transposase-Accessible Chromatin is based on the use of the transposase Tn5 which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification. Recomended sequencing depth 25-30M reads/sample. |
Internal
$177.37
each
UPenn $177.37 each Academic $195.10 each |
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DNA Chip-Seq (NEB) |
The Ultra II FS kit can be used for any DNA input amount (100 pg–500 ng), or GC content. |
Internal
$131.69
Sample
UPenn $131.69 Sample Academic $144.85 each |
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Illumina / NebNext Stranded mRNA (poly-A enrichment) |
Stranded total RNA kit supports a broad range of high quality RNA inputs, from 25 ng to 1000 ng. |
Internal
$141.35
Sample
UPenn $141.35 Sample Academic $155.48 Sample |
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Illumina Exome/Target Panel |
Library preparation for exome or other target pannel enrichment that accommodates low input amount DNA, 10-1000 ng high-quality genomic DNA or 50-1000 ng FFPE DNA. |
Internal
$286.63
Sample
UPenn $286.63 Sample Academic $315.30 Sample |
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Illumina stranded total RNA with Ribo-zero Plus |
Illumina Total RNA Prep with Ribo-Zero Plus supports a broad range of RNA, from 1 ng to 1ug of total RNA input. It is compatible with variable sample types, including formalin-fixed paraffin-embedded (FFPE) and other low-quality samples. |
Academic
$207.27
Sample
|
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Illumina WGS DNA PCR-Free Library Prep |
Illumina DNA PCR-Free workflow supports a broad DNA input range (100 ng to 1000 ng), uses bead-based tagmentation technology which delivers accurate base calling and variant identification. Blood, Low-Input, Saliva compatible, but Not FFPE-Compatible DNA samples. |
Internal
$141.39
Sample
UPenn $141.39 Sample Academic $155.53 Sample |
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Illumina WGS DNA Prep (6-8 PCR cycles) |
Illumina DNA Prep workflow supports a broad DNA input range (1–500 ng), multiple sample types, and both small and large genomes. The workflow includes DNA extracted from blood, saliva, or dried blood spots or bacterial colonies. On-bead tagmentation chemistry and library normalization. |
Internal
$119.65
Sample
UPenn $119.65 Sample Academic $132.00 Sample |
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Labor surcharge |
Library preparation service surcharge for projects with less than 12 samples |
Internal
$325.00
each
UPenn $325.00 each Academic $357.50 each |
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Qiagen QIAseq miRNA Library Prep. |
QIAseq miRNA Library Kit is optimized for ultralow RNA input (1ng-100ng). In addition, the kit integrates Unique Molecular Indices (UMIs) into the reverse-transcription process, enabling unbiased and accurate miRNome-wide quantification of mature miRNAs. Includes access to the RNA-seq Analysis Portal for human, mouse and rat samples |
Internal
$244.21
Sample
UPenn $244.21 Sample Academic $268.63 Sample |
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QuantSeq 3' mRNA-Seq Library Prep Kit FWD with Globin Block |
QuantSeq 3’ mRNA-Seq library prep generates NGS libraries of sequences close to the 3′ end of polyadenylated RNAs and requires only 0.5–500 ng of total RNA input without the need for poly(A) enrichment or ribosomal RNA depletion making it suitable for low quality RNA (including FFPE samples). Min 16 samples. |
Internal
$123.94
Sample
Academic $136.34 Sample |
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RiboCop (HMR) and CORALL Total RNA-Seq V2 Library Prep Kit |
Total RNA-Seq provides the optimal coverage for samples of varying quantity and quality and is perfectly suited for analyzing FFPE and Biobank samples, long non-coding RNA or perform bacterial transcriptomics after ribosomal RNA depletion. Total RNA without prior depletion or enrichment (100 pg to 100 ng) can also be used as input. |
Internal
$236.98
each
UPenn $236.98 each Academic $260.50 each |
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Whole Genome Bisulfite Sequencing (WGBS) Zymo |
The protocol is designed for 10 pg – 100 ng genomic DNA input. DNA should be free of enzymatic inhibitors. |
Internal
$162.49
each
UPenn $162.49 each Academic $179.30 each |
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► Nanopore Sequencing – PromethION (5) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
DNA sequencing (library preparation not included) |
DNA sequencing of sheared DNA fragments from 5 kb to 50 kb. Price per flow cell. Yields per PromethION flowcell can range from 20 Gb up to 100 Gb.
For long-read sequencing genomic DNA samples isolated with spin column protocols ( e.g. Qiagen DNeasy) are sufficient. Please submit at least 5µg of total DNA at a concentration of 100ng/µl in 50µl volume. The DNA isolation protocols should include an RNAse digestion. |
Internal
$1,017.00
each
UPenn $1,017.00 each Academic $1,119.70 each |
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DNA shearing |
We use g-TUBEs (Covaris) for shearing DNA 6kb to 20 kb. |
Internal
$45.00
each
UPenn $45.00 each Academic $49.50 each |
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Library preparation (DNA/RNA) |
Library preparation for PromethION sequencing, includes multiplexing to up to 24 samples. Only DNA/RNA of high quality can be sequenced. Library preparation does not include sample QC and DNA shearing, please provide QC for each sample, BioAnlyzer, Qubit and Nanodrop values are required. |
Internal
$141.00
each
Academic $155.00 each UPenn $141.00 each Corporate $184.00 each |
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RNA sequencing (library preparation not included) |
Sequencing of RNA with ligated sequencing adapters. Price per flow cell. Yields per flow cell of max 100 Gb. The PromethION Flow Cell contains up to 2675 nanopore channels for sequencing RNA in real time.
|
Internal
$1,017.00
each
UPenn $1,017.00 each Academic $1,118.70 each |
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Self-service sequencing on PromethION 24 |
Self service sequencing charges are per flow cell and only include instrument service. Investigators are responsable for the sequencing run (set up, monitoring, flow cell wash etc.) |
Internal
$100.00
each
UPenn $100.00 each |
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► NextSeq Self Service (1) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
NextSeq Self Service |
Please contact us to make an appointment for a self run on the NextSeq 1000. Bring your own reagent cartridge, flow cell and Library pool ready to be loaded on the instrument. Listed prices represent hourly charge for instrument use (covers instrument service contract). Please select the appropriate number of hours base on the flow cell and cycle number. NextSeq 1000 kits P1 (1x100/2x50)= 10 hours P1 (2x150)= 19 hours P2 (1x100/2x50)= 13 hours P2 (2x100)= 21 hours P2 (2x150)= 29 hours |
Internal
$20.00
each
UPenn $20.00 each |
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► NextSeq Services (7) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
NextSeq 1000/2000 P2 Reagents (100 Cycles) v3 |
Read length: 2x50 Output: 40 Gb Reads Passing Filter per flow cell: 400 Million |
Internal
$2,042.46
each
UPenn $2,042.46 each Academic $2,206.70 each |
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NextSeq 1000/2000 P2 Reagents (200 Cycles) v3 |
Read length: 2x100 Output: 80 Gb Reads Passing Filter per flow cell: 400 Million |
Internal
$3,630.94
each
UPenn $3,630.94 each Academic $3,994.00 each |
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NextSeq 1000/2000 P2 Reagents (300 Cycles) v3 |
Read length: 2x150 Output: 120 Gb Reads Passing Filter per flow cell: 400 Million |
Internal
$4,786.47
each
UPenn $4,786.47 each Academic $5,265.70 each |
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NextSeq™ 1000 P1 XLEAP-SBS™ Reagent Kit (100 Cycles) |
Read length: 2x50 Powered by XLEAP-SBS chemistry, provides kitted NextSeq 1000/2000 reagents for 100 cycles of sequencing, plus dual-indexing support (up to 100M reads) |
Internal
$1,158.00
each
UPenn $1,158.00 each Academic $1,264.00 each |
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NextSeq™ 1000 P1 XLEAP-SBS™ Reagent Kit (300 Cycles) |
Read length: 2x150 Powered by XLEAP-SBS chemistry, provides kitted NextSeq 1000/2000 reagents for 300 cycles of sequencing, plus dual-indexing support (up to 100M reads) |
Internal
$1,610.00
each
UPenn $1,610.00 each Academic $1,771.00 each |
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NextSeq™ 1000 P1 XLEAP-SBS™ Reagent Kit (600 Cycles) |
Read length: 2x300 Powered by XLEAP-SBS chemistry, provides kitted NextSeq 1000/2000 reagents for 600 cycles of sequencing, plus dual-indexing support (up to 100M reads)
|
Internal
$2,310.00
each
UPenn $2,310.00 each Academic $2,541.00 each |
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NextSeq™ 1000 P2 XLEAP-SBS™ Reagent Kit (600 Cycles) |
Read length: 2x300 Powered by XLEAP-SBS chemistry, provides kitted NextSeq 1000/2000 reagents for 600 cycles of sequencing, plus dual-indexing support (up to 400M reads) |
Internal
$3,811.52
each
Academic $4,293.00 each UPenn $3,811.52 each |
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► NovaSeq Self Service (2) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
Demultiplex Run (for self-service sequencing) |
Only if you want HTS Core to demutiplex your data. |
Inquire | ||||||||||||||||||||||||||
NovaSeq 6000 self service |
Please contact us to make an appointment for a self run on NovaSeq 6000. Bring your own Reagents and Library pool ready to be loaded on the instrument. Listed prices represent hourly charge for instrument use per run (covers instrument service). Please select the apropriate number of hours based on the flow cell and cycle number.
|
Internal
$40.00
each
UPenn $40.00 each Academic $44.00 each |
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► NovaSeq Services (12) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
NovaSeq 6000 S1 Reagent Kit v1.5 (100 cycles) |
Read length: 2x50 or 1x100 Output: 134–167 Gb Reads Passing Filter per flow cell: 1,500-1,600 Million
|
Internal
$5,509.64
each
UPenn $5,509.64 each Academic $6,061.00 each |
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NovaSeq 6000 S1 Reagent Kit v1.5 (200 cycles) |
Read length: 2x100 Output: 266–333 Gb Reads Passing Filter per flow cell: 1,500-1,600 Million |
Internal
$7,047.99
each
UPenn $7,047.99 each Academic $7,752.80 each |
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NovaSeq 6000 S1 Reagent Kit v1.5 (300 cycles) |
Read length: 2x150 Output: 400–500 Gb Reads Passing Filter per flow cell: 1,500-1,600 Million |
Internal
$7,869.25
each
UPenn $7,869.25 each Academic $8,657.00 each |
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NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) |
Read length: 2x50 or 1x100 Output: 333–417 Gb Reads Passing Filter per flow cell: 3,500-3,800 Million |
Internal
$9,744.75
each
UPenn $9,744.75 each Academic $10,719.50 each |
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NovaSeq 6000 S2 Reagent Kit v1.5 (200 cycles) |
Read length: 2x100 Output: 667–833 Gb Reads Passing Filter per flow cell: 3,500-3,800 Million |
Internal
$12,351.35
each
UPenn $12,351.35 each Academic $13,587.00 each |
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NovaSeq 6000 S2 Reagent Kit v1.5 (300 cycles) |
Read length: 2x150 Output: 1000–1250 Gb Reads Passing Filter per flow cell: 3,500-3,800 Million |
Internal
$13,697.64
each
UPenn $13,697.64 each Academic $15,068.00 each |
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NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles) |
Read length: 2x100 Output: 1600–2000 Gb Reads Passing Filter per flow cell: 8-10 Billion |
Internal
$17,671.37
each
UPenn $17,671.37 each Academic $19,439.00 each |
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NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles) |
Read length: 2x150 Output: 2400–3000 Gb Reads Passing Filter per flow cell: 8-10 Billion |
Internal
$19,891.96
each
UPenn $19,891.96 each |
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NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) |
Read length: 1x100/2x50 Output: 65–80 Gb Reads Passing Filter per flow cell: 700-800 Million |
Internal
$3,419.00
each
UPenn $3,419.00 each Academic $3,760.90 each |
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NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles) |
Read length: 2x100 Output: 134–167 Gb Reads Passing Filter per flow cell: 700-800 Million |
Internal
$4,538.75
each
UPenn $4,538.75 each Academic $4,993.00 each |
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NovaSeq 6000 SP Reagent Kit v1.5 (300 cycles) |
Read length: 2x150 Output:200–250 Gb Reads Passing Filter per flow cell: 700-800 Million |
Internal
$5,180.45
each
UPenn $5,180.45 each Academic $5,699.00 each |
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NovaSeq 6000 SP Reagent Kit v1.5 (500 cycles) |
Read length: 2x250 Output: 325–400 Gb Reads Passing Filter per flow cell: 700-800 Million |
Internal
$7,358.23
each
UPenn $7,358.23 each Academic $8,095.00 each |
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► NovaSeq™ X Series Self Service (1) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
Demultiplex Run (only for self service sequencing if needed) |
Service provided for self service sequencing, for all other sequencing services demultiplexing is included. |
Internal
$300.00
each
UPenn $300.00 each Academic $330.00 each |
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► NovaSeq™ X Series Services (1) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
NovaSeq™ X Series 25B Reagent Kit (300 Cyc) |
NovaSeq X Series Reagent Kits are powered by XLEAP-SBS chemistry: a faster, more accurate, and robust update to traditional sequencing by synthesis (SBS) This reagent kit provides one NovaSeq X Series 25 B flow cell (with 2 lanes) and reagent consumables to support a single flow cell 300 cycles run. Read length: 2x150 Output: 16Tb Reads Passing Filter per flow cell: 25 Billion |
Inquire | ||||||||||||||||||||||||||
► QC Bioanalyzer/TapeStation (10) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
Bioanalyzer Chip DNA_High-Sensitivity (11 samples/chip) |
Size Range: 50-7000 bp Quantitative Range: 5-1000 pg/µL Requires: 1 uL of sample, please submit an aliquot of 2 ul |
Internal
$110.00
Run
UPenn $110.00 Run Academic $121.00 each |
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Bioanalyzer Chip total RNA_nano (12 samples/chip) |
Size Range: 100-6000 bp Quantitative Range: 5-500ng/uL Requires: 1uL of sample, please submit an aliquot of 2 ul |
Internal
$110.00
Run
UPenn $110.00 Run Academic $121.00 each |
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Bioanalyzer Chip total RNA_pico (11 samples/chip) |
Size Range: 100-6000 bp Quantitative Range: 50-5000 pg/uL Requires: 1uL of sample, please submit an aliquot of 2 ul |
Internal
$110.00
Sample
UPenn $110.00 Sample Academic $121.00 each |
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DNA/RNA Qubit Quantification |
Requires 2ul volume per sample, please submit at least 3 ul of DNA/RNA per sample. |
Internal
$7.00
each
UPenn $7.00 each |
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Tape Station Genomic DNA Analysis 1st sample |
The gDNA ScreenTape assay can separate DNA samples from 200 to more than 60,000 base pairs
DIN Functional Range: 5-300ng/ul Quantitative Range: 10-100 ng/µL Requires 1ul volume per sample, please submit an aliquot of 2ul/sample |
Internal
$40.00
each
UPenn $40.00 each |
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Tape Station Genomic DNA Analysis, sample 2-15 |
The gDNA ScreenTape assay can separate DNA samples from 200 to more than 60,000 base pairs
DIN Functional Range: 5-300ng/ul Quantitative Range: 10-100 ng/µL Requires 1ul volume per sample, please submit an aliquot of 2ul/sample |
Inquire | ||||||||||||||||||||||||||
TapeStation High sensitivity DNA - D5000 1st sample |
Used for prepared libraries, dsDNA PCR products, fragmented DNA, etc
Size range: 100-5000 base pairs Quantitative range: 0.1-50 ng/ul Requires: 2uL of sample, please submit an aliquot of 3ul |
Internal
$36.00
Sample
UPenn $36.00 Sample |
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TapeStation High sensitivity DNA - D5000, sample 2-15 |
Used for prepared libraries, dsDNA PCR products, fragmented DNA, etc
Size range: 100-5000 base pairs Quantitative range: 0.1-50 ng/ul Requires: 2uL of sample, please submit an aliquot of 3ul |
Inquire | ||||||||||||||||||||||||||
TapeStation total RNA 1st sample |
Quantitative range: 25-500 ng/ul RIN functional range: 25-500 ng/ul Requires 2ul volume per sample, please submit an aliquot of 3ul |
Internal
$32.00
Sample
UPenn $32.00 Sample |
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TapeStation total RNA, sample 2-15 |
Quantitative range: 25-500 ng/ul RIN functional range: 25-500 ng/ul Requires 2ul volume per sample, please submit an aliquot of 3ul |
Inquire | ||||||||||||||||||||||||||
► Sequencing run set up (1) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
Sequencing run set up |
NextSeq/NovaSeq run set up (includes library pool QC via Bioanalyzer and Qubit and PhiX)
|
Internal
$110.00
each
UPenn $110.00 each Academic $121.00 each |
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► Surcharge (1) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
10% Hospital Surcharge (10% of total cost) |
Only for non CHOP/Penn Accademic institutions |
Academic
$1.00
each
|
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► qPCR (2) | ||||||||||||||||||||||||||||
Name | Description | Price | ||||||||||||||||||||||||||
KAPA DNA Quantification (qPCR for 1st sample) |
ROCHE PCR, qPCR, RT-PCR REAGENTS (includes plate, instrument run) |
Internal
$75.00
each
UPenn $75.00 each |
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KAPA DNA Quantification (qPCR for samples 2 - 40) |
ROCHE PCR, qPCR, RT-PCR REAGENTS |
Internal
$15.00
each
UPenn $15.00 each |
► Realtime PCR, Self-serve (4) | |||||||||||||||
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