Welcome!
The Sidney Kimmel Cancer Center Cancer Genomics Core Facility is a state-of-the-art, integrated, multi-site, shared resource consortium that was formed in 2016 through a merger of the Sidney Kimmel Cancer Center Cancer (SKCC) Cancer Genomics Core (SCGC) located at Thomas Jefferson University and the conjoint omics capabilities of the Center for Genomic Sciences (CGS) and the Center for Advanced Microbial Processing (CAMP) both of which are located within the Institute for Molecular Medicine and Infectious Diseases at Drexel University College of Medicine. The SKCC Cancer Genomics Shared Resource (CGSR) merges the capabilities of the two core facilities, together with the CGS and CAMP under the direction of Professor Brian Wigdahl PhD continuing operation at Drexel, and the SCGC under the direction ofHien Dang PhD continuing at TJU. This unique Shared Resource provides a collaborative interdisciplinary teaching and service environment which employs scientists and clinicians who provide consultative services in terms of experimental design and data analyses, as well as a very broad range of high-throughput and high-fidelity laboratory services.
The laboratory technical services include genomics, transcriptomics, and epigenetics with focus on single cell analysis at the TJU site and long read-sequencing as well as microbiome analysis at the Drexel site.
These facilities are dedicated to meeting the current and future needs of both researchers and clinicians and regularly implement new technologies and methods to provide the highest level of service. In addition, an integral role of the facility is to test new equipment and implement novel assays in collaboration with biotech companies. Included in these offerings are leading-edge capabilities in single cell analysis, ultra-long DNA sequencing, whole genome non-modified epigenetic analyses, and ultra-precise nucleic acid quantification technologies, all technologies that are rarely found in core facilities and which provide significant value-added to researchers with non-standard and complicated questions relating to oncogenesis.
The integration of the multiple omics methodologies within the SKCC Cancer Genomics Shared Resource wherein all of the faculty providers are co-localized provides for exceptional interdisciplinary expertise for the development of cross-cutting, complementary, and confirmatory studies with orthogonal technologies.
Instruments:
| NovaSeq 6000 Sequencing System | Revvity LabChip® GX Touch™ Nucleic Acid Analyzer |
| MiSeq Sequencing System | Levitas Bio LeviCell 1 cell isolation system |
| NextSeq Sequencing System | Nexcelom Cellometer K2 |
| NanoDrop ND-1000 Spectrophotometer | Miltenyi Biotec gentleMACS Octo Dissociator |
| Quant Studio 12K Flex PCR System | Miltenyi Biotec QuadroMACS Separator |
| COVARIS Focused Ultrasonicator | Thermofisher QuantStudio Q digital PCR |
| 10X Genomics Chromium Controller | BioRAD C1000 Touch Thermal Cycler X4 |
| 10X Genomics Chromium X | Eppendorf Centrifuge 5424R |
| 10X Genomics Cytassist | Thermofisher Qubit 4 Fluorometer |
| Agilent Bioanalyzer 2100 | Thermofisher Qubit Flex Fluorometer |
| Agilent Tapestation 4150 |
Services:
1.RNA sequencing : SKCC provides variety of bulk RNA sequencing services, such as stranded mRNA-seq, total RNA with Ribosomal depletion, small RNA-seq on Illumina instruments.
2.DNA sequencing: SKCC provides variety of DNA sequencing services, such as Whole Genome Sequencing, Whole Exome Sequencing, available or customized targeted Sequencing on Illumina instruments.
3.Single cell sequencing: SKCC utilize 10X genomics technology to provide variety of single cell services, such as 10x single cell RNAseq, 10X Linked Read Sequencing, 10x ATAC-Seq.
4.Spatial transcriptomics: SKCC provides variety of cutting-edge spatial services, such as Visium Spatial and Nanostring GeoMx samples sequencing
5. Cell preparation and nuclei acid isolation: SKCC provides service to facilitate single cell experiements and bulk sequencing processing, such RNA/DNA isolation from FFPE samples; live cell enrichment for scRNAseq processing.
For billing, we generally bill once project finishes, it's customers responsibility to update charge code and inform core members (Suhao Han) if need assistance with early billing/invoices.
For iLab related questions, please direct to Ryan Smally Ryan.Smalley@jefferson.edu. iLab tutorial: https://ewebapp01pa.jefferson.edu/kccresources/ilab-help/
*We do NOT provide service of storing biological samples; for courtesy of customers, we generally suggest customers to retrieve biological samples within 60 days after project finishes; We are not responsible to locate or reserve samples for more than 60 days.
Hien Dang, Ph.D., Director, Assistant Professor, hien.dang@jefferson.edu
Suhao Han, Ph.D., Research Associate, suhao.han@jefferson.edu
Emilie Lee, B.S., Research Assistant, Emilie.Lee@jefferson.edu
Dana Robbins, B.S., Research Assistant, dana.robbins@jefferson.edu
Garth Ehrlich, Co-Director, ge33@drexel.edu 215-762-1878
Carol Hope, Business Manager,clh353@drexel.edu 215-762-2959
Joshua Mell Deputy, Director, Genomics jcm385@drexel.edu 215-762-1445
Joshua Earl, Deputy Director, Bioinformatics, jpe39@drexel.edu 215-762-8133
Joris Beld, Deputy Director, Metabolomics & Proteomics, jb3669@drexelmed.edu 215-762-1735
Azad Ahmed, Laboratory Manager, Genomics, aia38@drexelmed.edu 215-762-1958
Bhaswati Sen, Laboratory Technician, Genomics bs563@drexel.edu
Rachel Ehrlich, Bioinformatician rle36@drexel.edu
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Thomas Jefferson University |
Drexel University 245 North 15th Street Philadelphia, PA 19102 Room 14309 |
|
Hours Open 9:00 am - 4:00 pm |
Hours Open 9:00 am - 6:00 pm |
| Name | Role | Phone | Location | |
|---|---|---|---|---|
| Hien Dang, PhD |
Co-Director
|
hien.dang@jefferson.edu
|
Bluemle Life Science Bldg
|
|
| Garth Ehrlich, PhD |
Co-Director
|
(215) 762-1878
|
ge33@drexel.edu
|
Drexel University College of Medicine
|
| Service List |
| ► TJU 10X Genomics Single Cell and VISIUM Library preparation (16) | |||
| Name | Description | Price | |
|---|---|---|---|
| TJU Chromium Flex Gene Expression GEM-X Experiment (16-32 rxn) |
|
SKCC Internal
$38,790.00
each
SKCC $38,790.00 each Thomas Jefferson $46,548.00 each External Academic $55,858.00 each External Commercial $67,029.00 each |
|
| TJU Chromium Flex Gene Expression GEM-X Experiment (for up to 16 rxns) |
|
SKCC Internal
$22,150.00
each
SKCC $22,150.00 each Thomas Jefferson $26,590.00 each External Academic $31,908.00 each External Commercial $38,289.00 each Custom(Extra) $0.00 each |
|
| TJU Chromium Flex Gene Expression GEM-X Experiment with Cell surface or sub-cellular protein (for up to 16 rxns) |
|
Inquire | |
| TJU Chromium GEM-X Single Cell 3' Kit v4 gene expression library preparation and QC |
Use 10X Genomics GEM-X Single Cell 3' Kit v4 for gene expression library preparation. Prefer in reactions/samples of 4X Targeted recovery cell number 5000-20,000. |
Inquire | |
| TJU Chromium NextGem Single Cell 3' gene expression Library preparation and QC |
Including QC RNA samples, lib prep with 10X genomics kit, final QC and Qubit for concentration and pooling library that will be ready for sequencing. Samples: 5000 cells per sample, viability >90% |
Inquire | |
| TJU Chromium Single Cell Immune Profiling (5') v3.0 GEM-X + CELL surface protein |
Use 10X Genomics Chromium Single Cell Immune Profiling (5') v3.0 GEM-X for gene expression profiling and same time with barcoded antibody for CELL surface protein profiling at the same chip run. Targeting recovery cell: 5000-20,000 Prefer sample/reactions number in multiple of 4. |
Inquire | |
| TJU Chromium Single Cell Immune Profiling (5') v3.0 GEM-X + CELL surface protein +TCR+BCR | Inquire | ||
| TJU Chromium Single Cell Multiome ATAC + Gene Expression | Inquire | ||
| TJU Single Cell 3' expression library preparation using 10x Genomics Chromium GEM-X Single Cell 3' Kit v4 with discount | Inquire | ||
| TJU single cell library preparation with existing quote |
Such as: Chromium GEM-X Single Cell 5' Reagent Kits v3 with Feature Barcode technology for Cell Surface Protein and BCR/TCR |
Inquire | |
| TJU Visium V2 CytAssist Spatial Gene Expression lib prep and QC, Human Transcriptome, 6.5 mm, 4 rxns (2 VISIUM slides) |
The serive is for 4 reactions/slides total!! The service includes:
The sample requirements:
|
Inquire | |
| TJU Visium Visium V2 CytAssist Spatial Gene Expression, Human Transcriptome, 11 mm, 2 rxns (1 slide) |
The serive is for 2 reactions in 1 slide total!! The service includes:
The sample requirements:
|
Inquire | |
| Visium HD, Human Transcriptome, 6.5mm, 4 rxns | Inquire | ||
| Visium HD, Mouse Transcriptome, 6.5mm, 4 rxns | Inquire | ||
| Visium V2 CytAssist Spatial Gene Expression for FFPE, Mouse Transcriptome, 11 mm, 2 rxns (1 slide) |
The serive is for 2 reactions in 1 slide total!! The service includes:
The sample requirements:
|
Inquire | |
| Visium V2 CytAssist Spatial Gene Expression for FFPE, Mouse Transcriptome, 6.5 mm, 4 rxns (2 slides) |
The sample requirements:
|
Inquire | |
| ► TJU NGS Library Preparation (13) | |||
| Name | Description | Price | |
| ATAC Library Kit |
SKCC Internal
$142.00
each
SKCC $142.00 each Thomas Jefferson $178.00 each External Academic $213.00 each External Commercial $256.00 each |
||
| CUT&RUN Assays |
SKCC Internal
$61.00
each
SKCC $61.00 each Thomas Jefferson $76.00 each External Academic $91.00 each External Commercial $110.00 each |
||
| CUT&Tag Assays |
SKCC Internal
$111.00
each
SKCC $111.00 each Thomas Jefferson $138.00 each External Academic $166.00 each External Commercial $199.00 each |
||
| Reduced Representation Bisulfite Sequencing (RRBS) |
SKCC Internal
$114.00
each
SKCC $114.00 each Thomas Jefferson $143.00 each External Academic $171.00 each External Commercial $206.00 each |
||
| TJU AmpliSeq BRCA Panel for Illumina |
Exonic regions and the flanking intronic sequences of the BRCA1 and BRCA2 Germline and somatic analysis studies of BRCA1 and BRCA2. 265 total. 2 pools. (Pool 1: 132 amplicons. Pool 2: 133 amplicons). DNA from Human tissue, including Blood, FFPE tissue DNA Input quantity: 1–100 ng (10 ng recommended per pool) |
SKCC Internal
$268.80
each
SKCC $268.80 each Thomas Jefferson $336.00 each External Academic $403.20 each External Commercial $483.60 each |
|
| TJU ChIP library preparation | Inquire | ||
| TJU DNA Exome library prep & QC and pooling |
Including QC samples, lib prep with Illumina® DNA Prep with Exome 2.0 Plus Enrichment kit (Human Exome), final QC and Qubit for concentration and pooling library that will be ready for sequencing. |
Inquire | |
| TJU small RNA Library Preparation & QC and pooling |
Including QC RNA samples, lib prep with NEBNext® Small RNA Library Prep Set for Illumina, final QC and Qubit for concentration and pooling library that will be ready for sequencing. |
SKCC Internal
$104.00
each
Thomas Jefferson $125.00 each External Academic $150.00 each External Commercial $180.00 each |
|
| TJU Total RNA Library Preparation & QC and pooling |
Including QC RNA samples, lib prep with Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit, final QC and Qubit for concentration and pooling library that will be ready for sequencing. |
SKCC Internal
$135.00
each
Thomas Jefferson $168.00 each External Academic $202.00 each External Commercial $242.00 each |
|
| TJU WES (Agilent SureSelect Max)-Human |
Utilize SureSelect Max Enzymatic Fragmentation Library Prep Kit, with SureSelect XT HS Human All Exon V8 for WES of human samples only. |
SKCC Internal
$410.00
each
SKCC $410.00 each Thomas Jefferson $512.00 each External Academic $614.00 each External Commercial $737.00 each Custom(Extra) $0.00 each |
|
| TJU WES (Agilent SureSelect Max)-Mouse only |
Utilize SureSelect Max Enzymatic Fragmentation Library Prep Kit, with SureSelect XT Community Design Mouse All Exon v2 for mouse samples only. |
SKCC Internal
$865.00
each
SKCC $865.00 each Thomas Jefferson $1,081.00 each External Academic $1,298.00 each External Commercial $1,557.00 each |
|
| TJU Whole Genome Library Preparation & QC and pooling |
Including QC samples, lib prep Illumina® DNA PCR-Free Prep kit, final QC and Qubit for concentration and pooling library that will be ready for sequencing. |
SKCC Internal
$78.00
each
Thomas Jefferson $94.00 each External Academic $113.00 each External Commercial $136.00 each |
|
| Whole Genome Bisulfite (WGBS) library preparation (standard gDNA input) |
|
SKCC Internal
$146.00
each
SKCC $146.00 each Thomas Jefferson $182.00 each External Academic $219.00 each External Commercial $263.00 each |
|
| ► TJU NGS Sequencing (24) | |||
| Name | Description | Price | |
| NovaSeq 6000 S1 Reagent Kit v1.5 (100 cycles) |
SKCC Internal
$5,227.00
each
Thomas Jefferson $6,272.00 each External Academic $7,512.00 each External Commercial $9,032.00 each |
||
| NovaSeq 6000 S1 Reagent Kit v1.5 (200 cycles) |
SKCC Internal
$7,184.40
each
SKCC $7,184.40 each Thomas Jefferson $7,184.40 each External Academic $7,903.20 each External Commercial $7,903.20 each |
||
| NovaSeq 6000 S1 Reagent Kit v1.5 (300 cycles) |
SKCC Internal
$7,776.00
each
SKCC $7,776.00 each Thomas Jefferson $7,776.00 each External Academic $8,553.60 each External Commercial $8,553.60 each |
||
| NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) | Inquire | ||
| NovaSeq 6000 S2 Reagent Kit v1.5 (200 cycles) |
SKCC Internal
$13,334.40
each
SKCC $13,334.40 each Thomas Jefferson $14,080.00 each External Academic $16,896.00 each External Commercial $16,896.00 each |
||
| NovaSeq 6000 S2 Reagent Kit v1.5 (300 cycles) | Inquire | ||
| NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles) |
SKCC Internal
$19,149.60
each
SKCC $19,149.60 each Thomas Jefferson $19,149.60 each External Academic $21,063.60 each External Commercial $21,063.60 each |
||
| NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles) |
customer provide library pool that can be sequenced on Illumina flatform. |
SKCC Internal
$21,336.00
each
SKCC $21,336.00 each Thomas Jefferson $21,336.00 each External Academic $23,469.60 each External Commercial $23,469.60 each |
|
| NovaSeq 6000 XP workflow |
Additional charge for novaseq 6000 XP workflow to split lines in flow cells. The charge is addtional to the flow cell cost, to cover XP workflow reagent cost. |
SKCC Internal
$1,874.00
each
SKCC $1,874.00 each Thomas Jefferson $2,248.00 each External Academic $2,698.00 each External Commercial $3,237.00 each |
|
| SP Reagent kit (100 cycles) | Inquire | ||
| SP Reagent kit (200 cycles) | Inquire | ||
| SP Reagent kit (300 cycles) | Inquire | ||
| TJU MiSeq v2 standard flow cell 500cycles | Inquire | ||
| TJU MiSeq v2 standard flow cell 2x150 | Inquire | ||
| TJU MiSeq v2 micro flow cell 2x150 | Inquire | ||
| TJU MiSeq v2 Nano Flow Cell 2x250 | Inquire | ||
| TJU MiSeq v2 Nano Flow Cell 2x150 | Inquire | ||
| TJU MiSeq v3 standard flow cell 2x300 | Inquire | ||
| TJU MiSeq v3 standard flow cell 2x75 | Inquire | ||
| TJU NextSeq 500 v2 Flow Cells High Output 2x150 |
SKCC Internal
$6,007.20
each
Thomas Jefferson $6,067.20 each External Academic $7,200.00 each External Commercial $7,800.00 each |
||
| TJU NextSeq 500 v2 Flow Cells Mid Output 2x75 | Inquire | ||
| TJU NextSeq 500 v2 Flow Cells High Output 1x75 |
SKCC Internal
$2,256.00
each
Thomas Jefferson $2,707.00 each |
||
| TJU NextSeq 500 v2 Flow Cells Mid Output 2x150 | Inquire | ||
| TJU NextSeq 500 v2 Flow Cells High Output 2x75 | Inquire | ||
| ► TJU Nucleic Acid Extraction (1) | |||
| Name | Description | Price | |
| RNA isolation from FFPE samples |
RNA isolation from FFPE samples for NGS lib prep and sequencing. |
SKCC Internal
$60.00
each
SKCC $60.00 each Thomas Jefferson $72.00 each External Academic $96.00 each External Commercial $96.00 each Custom(Extra) $26.40 each |
|
| ► TJU Quality Analysis (10) | |||
| Name | Description | Price | |
| Assay optimization |
The service include VISIUM oligo-conjugated antibodies assay optimization using |
Inquire | |
| Quality Analysis for RNAseq and smallRNAseq together |
Includes services of Tapestation RNA HS, Qubit HS RNA, Bioanalyzer small RNA |
Inquire | |
| TJU Agilent Bioanalyzer DNA High Sensitivity |
Increased sensitivity for DNA analysis, down to 5 pg/µL for fragment analysis or 100 pg/uL for complex DNA samples, such as NGS libraries. |
Inquire | |
| TJU Agilent Bioanalyzer Small RNA |
Small RNA electrophoresis with the 2100 Bioanalyzer System allows separation and quantitation measurements of challenging RNAs, such as microRNA and exosomes, sized below 200 nt and are often present in limited abundance. The Bioanalyzer Small RNA assay provides a fast and sensitive analysis to resolve small nucleic acid samples in the size range of 6 to 150 nt. |
Inquire | |
| TJU Agilent Tape Station DNA D1000 |
DNA from 35 to 1000 bp. DNA sample detection is possible down to 0.1 ng/µL. |
Inquire | |
| TJU Agilent Tape Station DNA D1000 High Sensitivity |
DNA from 35 to 1000 bp. Detection of DNA samples with limited abundance is possible, for samples down to 5 pg/µL. |
Inquire | |
| TJU Agilent Tape Station DNA D5000 |
DNA from 100 to 5000 bp. |
Inquire | |
| TJU Agilent Tape Station DNA D5000 High Sensitivity |
DNA from 100 to 5000 bp. |
Inquire | |
| TJU Agilent Tape Station RNA ScreenTape |
Utilizes RINe - a user independent algorithm for accurate and objective assessment of eukaryotic or prokaryotic total RNA integrity. Provides fast results with data delivered in approximately 1 minute per sample. Minimal sample consumption is required as only 1 µL of sample is needed for accurate data. RNA sample detection down to 5 ng/µL is possible. |
Inquire | |
| TJU Qubit |
DNA, RNA, and protein quantification it requires as little as 1 µL of sample |
Inquire | |
| ► TJU Quantitative PCR (1) | |||
| Name | Description | Price | |
| TJU Quant Studio 12K Flex Real-Time PCR | Inquire | ||
| ► unclassified (1) | |||
| Name | Description | Price | |
| LeviCell live cell enrichment |
Live cell enrichment reactions utilize LeviCell 1.0 system from LevitasBio to uncover pure, viable cells free of debris, and dead cells, which is ready for 10Xgenomics single cell processing. |
SKCC Internal
$200.00
each
SKCC $200.00 each Thomas Jefferson $240.00 each External Academic $288.00 each External Commercial $345.00 each |
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