Perelman School of Medicine | University of Pennsylvania
| NGSC - FAQs |
Next-Generation Sequencing Core Perelman School of Medicine | University of Pennsylvania |
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This example shows the cost of the smallest recommended experiment. There are two conditions with 3 samples each. The client just brings at least 500ng total RNA then the NGSC prepares the libraries and takes all other steps. Any of the steps before and after sequencing could be done by the client.
The labor charge is the maximum allowed. If we can process these samples in a batch with other samples, then the labor charge is reduced.
The pool of 6 samples is sequenced in a HiSeq 2500 lane using V4 chemistry (250 million reads) so the average read count per libary is about 40 million.
| Effective Date | 04/01/19 | |||||
| Total Estimated Cost | $4,763.75 | |||||
| Academic Cost | $6,192.88 | |||||
| Service Type | Service Code | Unit Price | Units | Count | Extended Price | Description |
| Informatics | IT-Analysis | $390.72 | each | 1 | $390.72 | Higher-level analysis pipeline, e.g., differential expression. CPU and data storage charges extra. |
| IT-RLB | $390.72 | lane | 1 | $390.72 | Basic pipeline run on a run-lane-barcode file. CPU and data storage charges extra. | |
| LibraryPrep-LT | Library Prep | $138.38 | sample | 6 | $830.28 | Low-throughput library prep using Illumina truSeq stranded mRNA kit. Labor extra. |
| LP-Labor | $100.00 | hour | 8 | $800.00 | Library prep labor per hour, applied to batches of library prep. | |
| QualityCheck | qc-Kapa | $45.00 | sample | 6 | $270.00 | Molarity measurement of library using Kapa Biosystems Library quant kit. 3 technical replicates of 3 dilutions of sample. |
| qc-Pooling | $1.00 | sample | 6 | $6.00 | Mix samples in equi-molar amounts to ensure as close to even read counts as possible. | |
| qc-bioAnalyzer | $25.00 | sample | 12 | $300.00 | RNA or library quality check with Agilent bioAnalyzer using any of the DNA or RNA chips. | |
| qc-qubit | $5.00 | sample | 6 | $30.00 | RNA or DNA concentration measurement using LifeTech qubit fluorimeter. | |
| Sequencing | sq-100SR-hiSeq-V4 | $1,746.03 | lane | 1 | $1,746.03 | Sequencing 1 ends, 100bp each, on HiSeq in high-output mode to get about 250 million reads or pairs |