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Epigenomics Shared Facility (ESF) Service Price List (2014-2015)

 

Whole Human Genome Sequencing:

We provide service for the whole human genome sequencing (30 X) using HiSeq X10 at NYGC for the cost of $1,575 per sample, plus Shipping and Handling.


1. Library Preparation For Massively Parallel Sequencing:

Service

 

Einstein

External

Assay

Sample Type

 Total Cost

12.5% Subsidy*

 Total Cost

Resequencing (whole genome, exome, targeted)

Genomic DNA

$400

$350

$600

Amplicon sequencing

PCR amplified DNA

$400

$350

$600

ChIP-seq

Immunoprecipitated chromatin and input DNA

$400

$350

$600

miRNA-seq

Total RNA

$400

$350

$600

Directional RNA-seq

Total RNA

$450

$394

$675

De novo assembly (mate pair library)

Genomic DNA

$750

$656

$1,125

HELP-GT (Genome-wide hydroxymethylation) /
HELPTagging (genome-wide methylation profiling)

Genomic DNA

$400

$350

$600

ATAC-Seq (genome-wide factor occupancy-epigenomic profiling of open chromatin)

Fresh Cells (500 - 50,000)

$300

$263

$450

 

1.1. Automated Library Preparation For Massively Parallel Sequencing:

Service

 

Einstein

External

Assay

Sample Type

 Total Cost

12.5% Subsidy*

 Total Cost

Resequencing (whole genome, exome, targeted)

Genomic DNA in batches

batch 1

1-16

$400

$350

$600

batch 2

17-32

$350

$306

$525

batch 3

33-48

$250

$219

$375

batch 4

49-64

$200

$175

$300

batch 5

65-80

$175

$153

$263

batch 6

81-96

$165

$144

$248

HELP-GT (Genome-wide hydroxymethylation) /
HELPTagging (genome-wide methylation profiling)

Genomic DNA in batches

batch 1

1-16

$400

$350

$600

batch 2

17-32

$360

$315

$540

batch 3

33-48

$320

$280

$480

batch 4

49-64

$280

$245

$420

batch 5

65-80

$240

$210

$360

batch 6

81-96

$220

$193

$330

ATAC-Seq (genome-wide factor occupancy-epigenomic profiling of open chromatin)

Fresh Cells (500 - 50,000)

batch 1

1-16

$300

$263

$450

batch 2

17-32

$260

$228

$390

batch 3

33-48

$220

$193

$330

batch 4

49-64

$200

$175

$300

batch 5

65-80

$180

$158

$270

batch 6

81-96

$160

$140

$240

RNA sequencing

Total RNA samples in batches

batch 1

1-16

$450

$394

$675

batch 2

17-32

$375

$328

$563

batch 3

33-48

$350

$306

$525

batch 4

49-64

$300

$263

$450

batch 5

65-80

$275

$241

$413

batch 6

81-96

$250

$219

$375

RNA sequencing-Low Input (~100 ng)

low Input RNA samples in batches

batch 1

1-16

$500

$438

$750

batch 2

17-32

$475

$416

$713

batch 3

33-48

$450

$394

$675

batch 4

49-64

$400

$350

$600

batch 5

65-80

$375

$328

$563

batch 6

81-96

$350

$306

$525

Amplicon sequencing

PCR amplified DNA in batches

batch 1

1-16

$325

$284

$488

batch 2

17-32

$195

$171

$293

batch 3

33-48

$130

$114

$195

batch 4

49-64

$110

$96

$165

batch 5

65-80

$100

$88

$150

batch 6

81-96

$90

$79

$135

 

2. Illumina HiSeq 2500 Sequencing Services1:

Service

 

Einstein

External

 

 

 Total Cost

12.5% Subsidy*

 Total Cost

Read Length

Recommended assays

50 bp

Single end (SE) sequencing cost/lane

HELP-tagging, miRNA-seq

$1,200

$1,050

$1,350

Paired end (PE) sequencing cost/lane 2

 

$1,800

$1,575

$2,000

Single end (SE) sequencing cost/flow cell**

 

$2,000

$1,750

$2,500

Paired end (PE) sequencing cost/flow cell**

 

$2,700

$2,363

$3,800

 

 

 

 

 

Read Length

 

100 bp

Single end (SE) sequencing cost/lane

RNA-seq, ChIP-seq

$1,600

$1,400

$1,800

Paired end (PE) sequencing cost/lane

resequencing, amplicon sequencing,

de novo assembly

$2,300

$2,013

$2,600

Single end (SE) sequencing cost/flow cell**

RNA-seq, ChIP-seq

$2,700

$2,363

$3,400

Paired end (PE) sequencing cost/flow cell**

resequencing, amplicon sequencing,

de novo assembly

$3,900

$3,413

$4,950

 

 

 

 

 

Read Length

 

150 bp2

Single end (SE) sequencing cost/lane

RNA-seq, ChIP-seq

$1,800

$1,575

$2,150

Paired end (PE) sequencing cost/lane

resequencing, amplicon sequencing,

Exome Capture sequencing, de novo assembly

$2,600

$2,275

$3,750

Single end (SE) sequencing cost/flow cell**

RNA-seq, ChIP-seq

$2,800

$2,450

$4,000

Paired end (PE) sequencing cost/flow cell**

resequencing, amplicon sequencing,

Exome Capture sequencing, de novo assembly

$4,400

$3,850

$6,600

 

 

 

 

 

Read Length

 

250 bp2‡

Single end (SE) sequencing cost/lane

amplicon, ChIP-seq

resequencing, otherseq

$2,300

$2,013

$3,450

Paired end (PE) sequencing cost/lane

resequencing, amplicon sequencing,

otherseq, de novo assembly

$3,200

$2,800

$4,800

Single end (SE) sequencing cost/flow cell**

amplicon, ChIP-seq

resequencing, otherseq

$3,600

$3,150

$5,400

Paired end (PE) sequencing cost/flow cell**

resequencing, amplicon sequencing,

otherseq, de novo assembly

$5,400

$4,725

$8,100

 

3. Illumina MiSeq Sequencing Services 3:

Service

Einstein

External

 

 Total Cost

12.5% Subsidy*

 Total Cost

Read Length

1 x 25-50 bp single end

2 x 25 bp paired end

Single end (SE) Sequencing cost/run

$850

$744

$1,275

Paired end (PE) Sequencing cost/run

$900

$788

$1,350

Read Length

1 x 75-100 bp single end

2 x 75 bp paired end

Single end (SE) Sequencing cost/run

$935

$818

$1,403

Paired end (PE) Sequencing cost/run

$1,000

$875

$1,500

Read Length

1 x 150 bp single end

2 x 150 bp paired end

Single end (SE) Sequencing cost/run

$1,050

$919

$1,575

Paired end (PE) Sequencing cost/run

$1,150

$1,006

$1,725

Read Length

1 x 250 bp single end

2 x 250 bp paired end

Single end (SE) Sequencing cost/run

$1,250

$1,094

$1,875

Paired end (PE) Sequencing cost/run

$1,400

$1,225

$2,100

Read Length

1 x 300 bp single end

2 x 300 bp paired end

Single end (SE) Sequencing cost/run

$1,570

$1,374

$2,355

Paired end (PE) Sequencing cost/run

$1,750

$1,531

$2,625

 

4. Multiplexing Charges 4:

Service

Einstein

External

 

 Total Cost

12.5% Subsidy*

 Total Cost

Multiplexing§ / 1-4 samples, cost/lane

$50

$44

$75

Multiplexing§ /5-8 samples, cost/lane

$100

$88

$150

Multiplexing§ /9-12 samples, cost/lane

$150

$131

$225

Multiplexing§ /13-24 samples, cost/lane

$200

$175

$300

Multiplexing§ /25-48 samples, cost/lane

$250

$219

$375

Multiplexing§ /49-96 samples, cost/lane

$300

$263

$450

* 12.5% subsidy is provided by Dean's office to all Einstein researchers for using Illumina sequencing services.

**Rapid run mode flow cell only have 2 lanes, which can be used with the on-instrument clustering option to run same individual or multiplexed samples in both lanes or different individual or multiplexed samples per lane which requires extra steps of DNA loading and annealing using cBot.

1 Number of reads expected/lane ~100-150 million.  Turnaround time 4-8 weeks, depending upon the type of assay and read length.

2 Only available in a rapid run mode: and must be provided enough samples to fill 2 lanes (whole flow cell). Turnaround time 1-2 weeks once the libraries are ready to sequence.

2‡ Only available in a rapid run mode: and must be provided enough samples to fill 2 lanes (whole flow cell). The 2x250 rapid run can generate up to 150 million reads and up to 75 Gb data per lane (150 Gb total/flow cell). Turnaround time 2 weeks once the libraries are ready to sequence.

3 Number of reads expected ~15 million single-end and 30 million paired-end run (~0.5 to 8.5 Gb data) with V2 reagents.  Turnaround time usually <1 week after library preparation. MiSeq run itself takes ~4 to 40 hours to complete depending upon the read length.

4 Truseq barcode adapters can be purchased from the ESF.

 

5. SeqCap Epi:


SeqCap Epi CpGiant

We provide services for SeqCap Epi, target enrichment of bisulfite treated DNA, to identify genome wide methylation variation assessment (Human), using Roche NimbleGen solution-based capture methods:

 

Read Length

2 x 100 bp

 

Einstein

External

Service

 Total Cost

12.5% Subsidy*

 Total Cost

Total cost for 3 samples (Library+Capture+Sequencing)

$4,000

$3,500

$5,080

Cost/sample1

$1,333

$1,167

$1,693

1 must submit minimum of 3 samples to process at one time for 30 x coverage. There are other options also available please contact ESF for further details.

Turnaround time: 6-8 weeks depending upon the number of samples.


SeqCap Epi Choice

The SeqCap Epi Choice assays are customized, utilizes selective probe pools that can target both strands of bisulfite treated human genomic DNA for targets up to 90Mb. We provide this service as project based please consult ESF about your project needs .

 

6. Exome-Seq:


Human

We use SeqCap EZ Exome Library v3.0 (NimbleGen) solution-based capture method that enables enrichment of the whole exome and miRNAs, based on the latest database builds and offering a 64 Mb sequence capture.

 

Read Length

2 x 100 bp

 

Einstein

External

Service

 Total Cost

12.5% Subsidy*

 Total Cost

Library cost /4sample

$1200

$1,050

$1800

Capture cost/4sample1

$645

$565

$968

Paired end (PE) sequencing cost/lane/4samples

$2,300

$2,013

$2,850

Total cost for 4 samples (Library+Capture+Sequencing)

$4,145

$3,627

$6,218

Cost/sample1

$1,036

$907

$1,554

1 must submit minimum of 4 samples to process at one time for ~50 x coverage. There are other options also available such as 30X or 100 X coverage, please contact ESF for pricing.

Turnaround time: 6-8 weeks depending upon the number of samples.

 

Mouse

We use SeqCap EZ Mouse Exome Design (NimbleGen) comprises over 54.3 Mb of target sequence (C57BL/6J, NCBI37/mm9) including 203,225 exonic regions and microRNAs.

 

Read Length

2 x 100 bp

 

Einstein

External

Service

 Total Cost

12.5% Subsidy*

 Total Cost

Total cost for 4 samples (Library+Capture+Sequencing)

$4,320

$3780

$5,560

Cost/sample1

$1,080

$945

$1,390

1 must submit minimum of 4 samples to process at one time for ~50 x coverage. There are other options also available such as 30 x or 100 x coverage, please contact ESF for pricing.

Turnaround time: 6-8 weeks depending upon the number of samples.

 

7. Custom Design Target Capture Sequencing:

Customer/user provides Choice Libraries (purchased fully by user) to use for capturing/enrich customer regions of interest. We recommend SeqCap EZ Choice Libraries (NimbleGen) to enrich customer regions of interest available in various sizes up to 50 Mb for human and other genomes. We also recommend to pool multiple samples to capture in one reaction however, it is users choice to decide the number of samples (libraries) to be pooled depending upon the desired fold coverage and the size of the target region. Below is some detail and the estimate of the capturing cost/sample for target capturing services by ESF:

 

 

Einstein

External

Multiplexing/Capture1

 Cost/Sample

12.5% Subsidy*

 Cost/Sample

1-sample/capture

$260

$227.5

$390

2-samples/capture

$135

$118

$203

3-samples/capture

$91

$80

$191

4-samples/capture

$65

$57

$98

6-samples/capture

$55

$48

$83

1 Please enquire at the Epigenomics Shared Facility (ESF) for more details.

Turnaround time: 6-8 weeks depending upon the number of samples.

 

8. Whole-genome Bisulfite Sequencing:

We provide services for whole-genome bisulfite sequencing (WGBS) for methylation analysis. Below is some detail and the estimate of the cost/sample by ESF:

 

Read Length

2 x 100 bp

 

Einstein

External

Service

 Total Cost

12.5% Subsidy*

 Total Cost

Total cost for 1 samples (Library+Sequencing) for up to 5 X coverage (~15Gb data)

$2,750

$2,406

$3,205

Total cost for 1 samples (Library+Sequencing) for up to 30 X coverage

$9,650

$8,444

$10,795

Please enquire at the Epigenomics Shared Facility (ESF) for more details.

Turnaround time: 6-8 weeks depending upon the number of samples.

 

Note: All prices subject to change. Please contact the facility prior to submission to confirm prices.