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Epigenetics Facility

The Epigenetics Core Facility provides a variety of research resources and services that include:

  • Nucleic acid extraction and fragmentation
  • Protein-nucleic acid association (ChIP) from tissue and enriched population
  • Quantitative gene expression analysis (qRT-PCR)
  • In situ hybridization detection of transcriptional targets with spatial resolution via RNAscope and Basescope.
  • Targeted DNA methylation analysis in specific genomic loci of interest,
  • Next generation sequencing library preparation (RNA-seq and ChIP-seq) and Illumina sequencing.

At Singel Cell level, we provide resources and services for both microfluidic-based and droplet-based single cell genomics (single cell gene expression, ATAC-seq and Multiome).

The facility also houses a sophisticated flow cytometry cell sorter that is equipped with 4 lasers and capable of detecting up to 11 colors. The sorter allows automated cytofluorimetric analysis and the sterile sorting of specific cell types, with biosafety protection.

This Core Facility uses iLab. Please click on the button below for instructions to request access and use our services.

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Facility Details

Instruments and Tools

Usage Rates

Please note all rates are effective September 1, 2024. Please contact us directly for prior rates.

QuantStudio 7 Flex Real-time qPCR system
CUNY Rate per Plate Non-CUNY Academic Rate Per Plate Industrial Rate per Plate
384 well plate $30 $33 $90
TLDA card $33 $36 $99

Nucleic Acid Isolation
CUNY Rate Per Sample Non-CUNY Academic Rate Per Sample Industrial Rate Per Sample
RNA isolation $40 $44 $120
RNA isolation + cDNA synthesis $51 $56 $153

PipetMAX
CUNY Rate Non-CUNY Academic Rate Industrial Rate
Self-operated $6 $7 $18

Qubit 3.0 Fluorometer
CUNY Rate Non-CUNY Academic Rate Industrial Rate
Annual fee only $42 $46 $126

Nanodrop One
CUNY Rate Non-CUNY Academic Rate Industrial Rate
Annual fee only $110 $121 $330

Biorupter Pico Sonication System
CUNY Rate Non-CUNY Academic Rate Industrial Rate
Annual fee only $185 $205 $555

TapeStation 4200
CUNY Rate Per Tape Non-CUNY Academic Rate Per Tape Industrial Rate Per Tape
D1000 or D5000 $91 $100 $273
D1000 HS or D5000 HS $107 $118 $321
Genomic DNA $107 $118 $321
RNA $95 $105 $285
RNA HS $115 $127 $345
Notes:

  • Each tape accommodates up to 15 samples and 1 ladder. Users are charged per tape even if the entire tape is not used.
  • Rates above include instrument usage, reagents and supplies.
  • Reagents and supplies can also be purchased separately.

AriaFusion Cell Sorter
CUNY Rate Per Hour Non-CUNY Academic Rate Per Hour Industrial Rate Per Hour
Self-operated $75 $85 $225
Staff-operated $135 $150 $405
Notes:

  • Sorting fee includes one-hour setup fee and the instrument usage fee.
  • The minimum charge for the instrument is 30 minutes.

PippinHT
CUNY Rate Per Cassette Non-CUNY Academic Rate Per Cassette Industrial Rate Per Cassette
Cassette (1.5%, 2%, or 3%) $200 $220 $600
Notes:

  • Rates above include reagents and supplies.

MassArray System with Epityper DNA Methylation Analysis
CUNY Rate Non-CUNY Academic Rate Industrial Rate
SpectroCHIP II (one chip with 96 amplicon capacity) $254 $275 $762
Methylation Analysis by MassArray (per amplicon) $12 $14 $36
For users who need the core to perform bisulfite treatment and PCR for individual amplicons, please refer to sample submission guidelines and the rates below.
Bisulfite conversion (per sample) $16 $18 $48
PCR amplification (per amplicon) $4 $5 $12
Notes:

  • The chip for Epityper contains 96 spots for analysis of 96 amplicons. User will be charged for the whole number of chips even if one entire chip is not used.
  • Methylation assay will be charged individually.

Illumina Next Generation Sequencing
CUNY Rate Non-CUNY Academic Rate Industrial Rate
mRNA-seq library prep $160 $176 $480
RiboErase depletion-seq library prep $250 $275 $750
ChIP-seq library prep $190 $240 $570
Illumina 2x150bp, ~350 million reads, dual index $1,500 $1,650 $2,250
Notes:

Partek Flow
CUNY Rate Non-CUNY Academic Rate Industrial Rate
Hourly Rate (Minimum 3 hours required) $13 $15 $39
Daily Rate (More than 7 hours in a 24 hour period) $95 $105 $285
Notes:

  • Each user will be assigned 250GB of storage space. Additional storage space may be acquired at user’s own cost.
  • Please reserve in Badger before using.

RNAscope
RNAscope – Fluorescence assay (probes supplied by user)
CUNY Rate Non-CUNY Academic Rate Industrial Rate
Single plex $194 $214 $582
Duplex $210 $231 $630
3-plex $225 $247 $675
4-plex $240 $264 $720
BaseScope – Chromogenic assay (Probes supplied by user)
Singleplex $150 $165 $450
Notes:

  • Rates above include instrument usage and reagents needed for the assay.
  • Rates above do NOT include the probes, which are supplied by the users.
  • Rates above are based on sections within 7-15 um thick and within 0.75 inch x 0.75 inch in size. Additional charges may apply if sections exceed the size limit.
  • Please refer to the tissue preparation and sample submission guidelines for preparing sections and fill out sample submission form.
Co-detection with Immunohistochemistry – Fluorescence assay (Antibodies supplied by user)

Rates are in addition to RNAscope/Basescope base rate.
Co-detection $46 $51 $138
Notes:

    • Can be combined with both RNAscope Fluorescent and Basescope Chromogenic assays.
    • Rates above do NOT include antibodies, which are supplied by the users.
    • A list of core validated antibodies can be found here. Antibodies not on the list cannot be guaranteed for successful assays.

10X
Single Cell Gene Expression
Number of samples Number of cells recovered/sample Number of reads/cell CUNY Rate per sample Non-CUNY Academic Rate per sample Industrial Rate per sample
2 5,000 >50,000 $3,877 $4,265 $7,228
4 5,000 >50,000 $2,884 $3,172 $5,098
8 5,000 >50,000 $2,600 $2,858 $4,365
2-3 10,000 >50,000 $3,877 $4,265 $7,228
4 10,000 >50,000 $3,306 $3,636 $5,761
8 10,000 >50,000 $3,036 $3,339 $5,052
Notes:

  • Rates above include instrument usage, reagents and paired-end sequencing.
  • Please contact us before submitting samples.
  • Please contact us for other sample numbers or special requirements of reads/cell.
Single Cell Multiome ATAC+ Gene expression – Please inquire before sample submission
Number of samples Number of cells recovered/sample Number of reads/cell CUNY Rate per sample Non-CUNY Academic Rate per sample Industrial Rate per sample
2 5,000 >50,000 $5455 $6000 $9990
3 5,000 >50,000 $5297 $5826 $9267
4 5,000 >50,000 $4796 $5275 $8243
8 5,000 >50,000 $4500 $4950 $7393
2 10,000 >50,000 $6298 $6928 $11315
3-4 10,000 >50,000 $5671 $6238 $9616
8 10,000 >50,000 $4937 $5431 $8080

C1 Single-Cell Auto Prep System
CUNY Rate Non-CUNY Academic Rate Industrial Rate
Single-cell Isolation and STA cDNA Preparation – 96 cells $1,300 $1,430 $3,900
Single-cell Isolation and RNA-seq cDNA Preparation + Illumina Sequencing Library Prep – 96 cells $3,100 $3,410 $9,300
Single-cell Isolation and RNA-seq cDNA Preparation + Illumina Sequencing Library Prep – 800 cells $4,400 $4,840 $13,200
Notes:

  • Rates above include reagents and instrument usage fee.
  • Rates above do NOT include sequencing fee.
  • Please contact us before submitting samples.

Biomark HD
CUNY Rate Non-CUNY Academic Rate Industrial Rate
96.96 Dynamic Array $1,580 $1,738 $4,740
Notes:

  • Rates above include reagents for Biomark IFC and instrument usage fee.
  • Rates above do NOT include any gene probe sets.
  • Please contact us before submitting samples.

For more information, please contact:

  • Jia Liu, Ph.D.
    • Director, Epigenetics Facility
    • Director, Rodent Behavioral Analysis Suite
    • Research Associate Professor, Neuroscience Initiative
     Email: jliu1@gc.cuny.edu
    Phone: 212.413.3183
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