Prices quoted are for Whitehead Institute/MIT only. In order to cover additional costs associated with providing outside service, non-WI/MIT institutions should add 30% to the list price.

= Sequencing =

There are three options for Illumina sequencing. NovaSeq and MiSeq.

Prices include basic data processing including base calls, quality scores and alignment (if requested).

Please visit the [http://gtc.wi.mit.edu/genomecorewiki/index.php/Sequencing Sequencing Services] page for sample submission instructions and more information about library prep services.

== Short Read (Single lane submissions accepted for standard read lengths) ==

=== Illumina NovaSeq ===

{| style="text-align: center; width:1000px; font-size:120%; border:3px dashed red;" border="1" align="center"
|-
| Item || Read Length || Unit || Price Per Unit || Notes
|-
|rowspan="4"|NovaSeqSP
| 100 Single End or 50x50 Paired-End
|rowspan="4"| 1 lane
|$1,850
|rowspan="4"|~650–800 million reads per flowcell ~325-400 million reads per lane (x2 for Paired-End)
|-
| 200 Single End or 100x100 Paired-End
|$2,245
|-
| 300 Single End or 150x150 Paired-End
|$2,620
|-
| 500 Single End or 250x250 Paired-End
|$3,510
|-
|rowspan="3"|NovaSeqS1
| 100 Single End or 50x50 Paired-End
|rowspan="3"|1 lane
|$2,920
|rowspan="3"|~1.3–1.6 billion reads per flowcell ~650–800 million reads per lane (x2 for Paired-End)
|-
| 200 Single End or 100x100 Paired-End
|$3,730
|-
| 300 Single End or 150x150 Paired-End
|$4,065
|-
|rowspan="3"|NovaSeqS2
| 100 Single End or 50x50 Paired-End
|rowspan="3"|1 lane
|$5,200
|rowspan="3"|~3.3–4.1 billion reads per flowcell ~1.65-2.05 billion reads per lane (x2 for Paired-End)
|-
| 200 Single End or 100x100 Paired-End
|$6,480
|-
| 300 Single End or 150x150 Paired-End
|$6,750
|-
|rowspan="2"|NovaSeqS4
| 50 Single End
|rowspan="2"|1 lane
|$3,780
|rowspan="2"|~8-10 billion reads per flowcell ~2-2.5 billion reads per lane (x2 for Paired-End)
|-
| 300 Single End or 150x150 Paired-End
|$5,400
|-
|}

 

=== Element AVITI ===
{{PricingHeader}}
{{PricingRow|150 Single End or 75x75 Paired End|Lane|$1,000| 400 million reads}}
{{PricingRow|300 Single End or 150x150 Paired End|Lane|$1,375| 400 million reads}}
{{PricingLastRow|300x300 Paired End|Flowcell|$3,500| 300 million reads}}

 

=== Illumina MiSeq ===
{{PricingHeader}}
{{PricingRow|MiSeq v2 70 Single End or 30x30 Paired End|Flowcell|$1,320| 10 million reads}}
{{PricingRow|MiSeq v3 150 Single End or 75x75 Paired End|Flowcell|$1,430| 20 million reads}}
{{PricingRow|MiSeq v2 300 Single End or 150x150 Paired End|Flowcell|$1,595| 10 million reads}}
{{PricingRow|MiSeq v2 500 Single End or 250x250 Paired End|Flowcell|$1,760| 10 million reads}}
{{PricingLastRow|MiSeq v3 600 Single End or 300x300 Paired End|Flowcell|$2,200| 20 million reads}}

 

== Long Read ==

=== Nanopore (P2 Solo/promethION) ===
{{PricingHeader}}
{{PricingLastRow|Nanopore|Flowcell|$1200| Upto 50 to 70GB data per flow cell}}

 

=== Pacbio ===
{{PricingHeader}}
{{PricingLastRow|Pacbio SMRTCell 25 Million|Run|$2900|Around 6 million reads, outsourcing to sister facilities to enable access to the REVIO}}

 

= RNA Library Prep =
=== Standard (Manual) ===
{{PricingHeader}}
{{PricingRow|IDT xGen RNA, Std or Rapid (formerly Swift), samples 1-12|Sample|$200|}}
{{PricingRow|IDT xGen RNA, Std or Rapid (formerly Swift), samples 13+|Sample|$150|}}
{{PricingRow|Watchmaker QiaSeq FastSelect Ribodepletion, samples 1-12|Sample|$200|}}
{{PricingRow|Watchmaker QiaSeq FastSelect Ribodepletion, samples 13+|Sample|$150|}}
{{PricingRow|Watchmaker mRNA, samples 1-12|Sample|$150|}}
{{PricingRow|Watchmaker mRNA, samples 13+|Sample|$100|}}
{{PricingRow|Agilent SureSelect All Exon|Sample|$650|}}
{{PricingLastRow|NEBNext Small RNA|Sample|$200|}}

 

=== Low Input (Manual) ===
{{PricingHeader}}
{{PricingLastRow|Clontech SMARTer UltraLow RNA w/ NexteraXT|Sample|$300|}}

 

=== Highthroughput (96 well Plate Based) ===

{| style="text-align: center; width:1000px; font-size:120%; border:3px dashed red;" border="1" align="center"
|-
| Item || Unit || Price Per Unit || Notes
|-
|rowspan="3"|HT mRNA library prep (IDT xGen RNA)
| 48 Samples
|$3600
|rowspan="3" width=50%| Samples should be pre-aliquoted (in Eppendorf twin.tec semi-skirted 96 well plate), normalized (100 and 500 ng total), in a volume of 50 ul.
Intake QC or quantification only by special arrangement at an additional charge. please inquire if needed.

Libraries are pooled by FA quantification, expect variation in read balancing.
|-
| 49-72 samples
|$5400
|-
| 96 samples
|$7200
|-
|}

 

= Single Cell (10X and others) =
{{PricingHeader}}
{{PricingRow|10X Single Cell 3’ GEX (Includes OCM if requested)|sample|$2560|}}
{{PricingRow|10X Single Cell 5’ GEX|sample|$2560|}}
{{PricingRow|10X VDJ Add-on|sample|$230|Can be added onto the 10X 5' GEX Only}}
{{PricingRow|10X CRISPR Add-on|sample|$280|Can be added onto the 10X 5' GEX Only}}
{{PricingRow|10X Antibody/CellPlex/MultiSeq Add-on|sample|$140|}}
{{PricingRow|10X Multiome Assay (ATAC + 3')|sample|$4200|}}
{{PricingRow|10X Flex (Fixed Cell)|sample|$2800|Human and Mouse Only}}
{{PricingRow|Plexwell Rapid Single Cell - one 96 well plate|96 well plate|$5060|1 cell per well}}
{{PricingLastRow|Plexwell Rapid Single Cell - 1 of 4 96 well plates|96 well plate|$3800|1 cell per well}}

 

= DNA Library Prep =
{{PricingHeader}}
{{PricingRow|Nextera gDNA (Genomic, ATAC-Seq)|sample|$200|"Tagmentation" prep from intact gDNA (50ng)}}
{{PricingLastRow|Illumina DNA Prep (Genomic)|sample|$200|Genomic DNA >100ng}}

 

= RNA Isolation =
{{PricingHeader}}
{{PricingRow|[http://genomecore.wi.mit.edu/index.php/rnaextraction RNA-miRNeasy Total RNA Isolation]|sample|$100|}}
{{PricingRow|[http://genomecore.wi.mit.edu/index.php/rnaextraction RNA - MagMax mirVana RNA Isolation]|sample|$30|}}
{{PricingLastRow|[http://genomecore.wi.mit.edu/index.php/rnaextraction RNA - Direct-zol™-96 MagBead RNA Isolation]|sample|$30|}}

 

= Quality Control =
{{PricingHeader}}
{{PricingRow|Bioanalyzer/Fragment Analyzer|1 to 20 Samples|$15|Sizing and purity analysis}}
{{PricingRow|Fragment Analyzer (half 96 well plate)|20 to 48 Samples|$300|Sizing and purity analysis}}
{{PricingRow|Fragment Analyzer (Full 96 well plate)|49+ Samples|$500|Sizing and purity analysis}}
{{PricingRow|qPCR|Sample|$25|Quantification}}
{{PricingLastRow|Sample Multiplexing|Sample|$10|Mixing samples for multiplex run}}

 

= Bioanalyzer - RNA, DNA and Protein analysis =
{{PricingHeader}}
{{PricingLastRow|RNA or DNA|Sample|$15|Pico, Nano, DNA or hsDNA}}

 

= Quantitative PCR - QuantStudio 6 =
{{PricingHeader}}
{{PricingRow|SYBR green / Taq Man Master mix|uL|7 cents|-}}
{{PricingRow|Optical Plate|Plate|$7|-}}
{{PricingLastRow|Equipment Time (2 hour time block)|Plate|$50|Sign-up Required}}

 

= Digital PCR =
{{PricingHeader}}
{{PricingLastRow|Equipment Time (2 hour time block)|Plate|$50|Sign-up Required}}

2024-07-10T22:08:03Z

Sgupta:

LibraryPrep

2024-07-10T22:07:47Z

Sgupta:

= Library prep =
== RNA ==
=== Watchmaker for mRNA ===
For standard expression analysis. Includes polyA selection of mRNA. Data is strand-specific. 10-500ng total RNA.

=== Watchmaker for Ribodepletion ===
Instead of polyA selection of mRNA this kit specifically removes ribosomal RNA leaving behind mRNA and long non-coding RNA. Best for whole transcriptome (polyA and other transcripts) analysis.

=== Watchmaker for Ribodepletion ===
Instead of polyA selection of mRNA this kit specifically removes ribosomal RNA leaving behind mRNA and long non-coding RNA. Best for whole transcriptome (polyA and other transcripts) analysis.

=== NEBnext small RNA ===
For microRNA and other small RNA. 100-1000ng total RNA.

=== Clonetech SMART-Seq v4 Ultra-low ===
For very low input RNA down to single cell. Data is NOT strand-specific. 10pg-10ng total RNA.

=== IDT/xGen for mRNA (Supported Only For Legacy Projects) ===
For standard expression analysis. Includes polyA selection of mRNA. Data is strand-specific. 10-500ng total RNA.

=== KAPA Hyperprep mRNA (Supported Only For Legacy Projects) ===
For standard expression analysis. Includes polyA selection of mRNA. Data is strand-specific. 100-500ng total RNA.

=== KAPA Hyperprep with Ribo-depletion (Supported Only For Legacy Projects) ===
Instead of polyA selection of mRNA this kit specifically removes ribosomal RNA leaving behind mRNA and long non-coding RNA. Best for whole transcriptome (polyA and other transcripts) analysis. Data is strand-specific. 100-1000ng total RNA (more is better)

=== Clonetech SMARTer PICO (Supported Only For Legacy Projects) ===
For low input of degraded RNA. Data is strand-specific. 10-100ng total RNA.

== DNA ==

=== Nextera gDNA ===
“Tagmentation” protocol for genomic or other DNA. Good for genomic DNA, ATAC-seq and other higher input DNA applications.

== Frequently Asked Questions ==
Please refer to [[Faq#Bulk_RNA-Seq|frequently asked questions section for FAQ regarding]] library prep options.

Pricing

2024-07-10T22:07:41Z

Sgupta:

Prices quoted are for Whitehead Institute/MIT only. In order to cover additional costs associated with providing outside service, non-WI/MIT institutions should add 30% to the list price.

= Illumina Sequencing =

There are three options for Illumina sequencing. NovaSeq and MiSeq.

Prices include basic data processing including base calls, quality scores and alignment (if requested).

Please visit the [http://jura.wi.mit.edu/genomecorewiki/index.php/Sequencing Sequencing Services] page for sample submission instructions and more information about library prep services.

=== Illumina NovaSeq (Single lane submissions accepted for standard read lengths) ===

{| style="text-align: center; width:1000px; font-size:120%; border:3px dashed red;" border="1" align="center"
|-
| Item || Read Length || Unit || Price Per Unit || Notes
|-
|rowspan="4"|NovaSeqSP
| 100 Single End or 50x50 Paired-End
|rowspan="4"| 1 lane
|$1,850
|rowspan="4"|~650–800 million reads per flowcell ~325-400 million reads per lane (x2 for Paired-End)
|-
| 200 Single End or 100x100 Paired-End
|$2,245
|-
| 300 Single End or 150x150 Paired-End
|$2,620
|-
| 500 Single End or 250x250 Paired-End
|$3,510
|-
|rowspan="3"|NovaSeqS1
| 100 Single End or 50x50 Paired-End
|rowspan="3"|1 lane
|$2,920
|rowspan="3"|~1.3–1.6 billion reads per flowcell ~650–800 million reads per lane (x2 for Paired-End)
|-
| 200 Single End or 100x100 Paired-End
|$3,730
|-
| 300 Single End or 150x150 Paired-End
|$4,065
|-
|rowspan="3"|NovaSeqS2
| 100 Single End or 50x50 Paired-End
|rowspan="3"|1 lane
|$5,200
|rowspan="3"|~3.3–4.1 billion reads per flowcell ~1.65-2.05 billion reads per lane (x2 for Paired-End)
|-
| 200 Single End or 100x100 Paired-End
|$6,480
|-
| 300 Single End or 150x150 Paired-End
|$6,750
|-
|rowspan="2"|NovaSeqS4
| 50 Single End
|rowspan="2"|1 lane
|$3,780
|rowspan="2"|~8-10 billion reads per flowcell ~2-2.5 billion reads per lane (x2 for Paired-End)
|-
| 300 Single End or 150x150 Paired-End
|$5,400
|-
|}

 

=== Element AVITI ===
{{PricingHeader}}
{{PricingRow|150 Single End or 75x75 Paired End|Lane|$1,000| 400 million reads}}
{{PricingRow|300 Single End or 150x150 Paired End|Lane|$1,375| 400 million reads}}
{{PricingLastRow|300x300 Paired End|Flowcell|$3,500| 800 million reads}}

 

=== Illumina MiSeq ===
{{PricingHeader}}
{{PricingRow|MiSeq v2 70 Single End or 30x30 Paired End|Flowcell|$1,320| 10 million reads}}
{{PricingRow|MiSeq v3 150 Single End or 75x75 Paired End|Flowcell|$1,430| 20 million reads}}
{{PricingRow|MiSeq v2 300 Single End or 150x150 Paired End|Flowcell|$1,595| 10 million reads}}
{{PricingRow|MiSeq v2 500 Single End or 250x250 Paired End|Flowcell|$1,760| 10 million reads}}
{{PricingLastRow|MiSeq v3 600 Single End or 300x300 Paired End|Flowcell|$2,200| 20 million reads}}

 

= RNA Library Prep =
=== Standard (Manual) ===
{{PricingHeader}}
{{PricingRow|IDT xGen RNA, Std or Rapid (formerly Swift), samples 1-12|Sample|$200|}}
{{PricingRow|IDT xGen RNA, Std or Rapid (formerly Swift), samples 13+|Sample|$150|}}
{{PricingRow|KAPA Hyper Prep Ribo Zero, samples 1-12|Sample|$250|}}
{{PricingRow|KAPA Hyper Prep Ribo Zero, samples 13+|Sample|$200|}}
{{PricingRow|Watchmaker mRNA, samples 1-12|Sample|$150|}}
{{PricingRow|Watchmaker mRNA, samples 13+|Sample|$100|}}
{{PricingRow|Agilent SureSelect All Exon|Sample|$650|}}
{{PricingLastRow|NEBNext Small RNA|Sample|$200|}}

 

=== Low Input (Manual) ===
{{PricingHeader}}
{{PricingLastRow|Clontech SMARTer UltraLow RNA w/ NexteraXT|Sample|$300|}}

 

=== Highthroughput (96 well Plate Based) ===

{| style="text-align: center; width:1000px; font-size:120%; border:3px dashed red;" border="1" align="center"
|-
| Item || Unit || Price Per Unit || Notes
|-
|rowspan="3"|HT mRNA library prep (IDT xGen RNA)
| 48 Samples
|$3600
|rowspan="3" width=50%| Samples should be pre-aliquoted (in Eppendorf twin.tec semi-skirted 96 well plate), normalized (100 and 500 ng total), in a volume of 50 ul.
Intake QC or quantification only by special arrangement at an additional charge. please inquire if needed.

Libraries are pooled by FA quantification, expect variation in read balancing.
|-
| 49-72 samples
|$5400
|-
| 96 samples
|$7200
|-
|}

 

= Single Cell (10X and others) =
{{PricingHeader}}
{{PricingRow|10X Single Cell 3’ GEX|sample|$2560|}}
{{PricingRow|10X Single Cell 5’ GEX|sample|$2560|}}
{{PricingRow|10X VDJ Add-on|sample|$230|Can be added onto the 10X 5' GEX Only}}
{{PricingRow|10X ADT/HTO/CellPlex Add-on|sample|$140|}}
{{PricingRow|10X Multiome Assay (ATAC + 3')|sample|$4200|}}
{{PricingRow|10X Flex (Fixed Cell)|sample|$2800|Human and Mouse Only}}
{{PricingRow|Plexwell Rapid Single Cell - one 96 well plate|96 well plate|$5060|1 cell per well}}
{{PricingLastRow|Plexwell Rapid Single Cell - 1 of 4 96 well plates|96 well plate|$3800|1 cell per well}}

 

= DNA Library Prep =
{{PricingHeader}}
{{PricingRow|Nextera gDNA (Genomic, ATAC-Seq)|sample|$200|"Tagmentation" prep from intact gDNA (50ng)}}
{{PricingLastRow|Illumina DNA Prep (Genomic)|sample|$200|Genomic DNA >100ng}}

 

= RNA Isolation =
{{PricingHeader}}
{{PricingRow|[http://genomecore.wi.mit.edu/index.php/rnaextraction RNA-miRNeasy Total RNA Isolation]|sample|$100|}}
{{PricingLastRow|[http://genomecore.wi.mit.edu/index.php/rnaextraction RNA - MagMax mirVana RNA Isolation]|sample|$30|}}

 

= Quality Control =
{{PricingHeader}}
{{PricingRow|Bioanalyzer|Sample|$15|Sizing and purity analysis}}
{{PricingRow|qPCR|Sample|$25|Quantification}}
{{PricingLastRow|Sample Multiplexing|Sample|$10|Mixing samples for multiplex run}}

 

= Bioanalyzer - RNA, DNA and Protein analysis =
{{PricingHeader}}
{{PricingLastRow|RNA or DNA|Sample|$15|Pico, Nano, DNA or hsDNA}}

 

= Quantitative PCR - QuantStudio 6 =
{{PricingHeader}}
{{PricingRow|SYBR green / Taq Man Master mix|uL|7 cents|-}}
{{PricingRow|Optical Plate|Plate|$7|-}}
{{PricingLastRow|Equipment Time (2 hour time block)|Plate|$30|Sign-up Required}}

LibraryPrep

2024-07-10T21:58:28Z

Sgupta:

= Library prep =
== RNA ==
=== KAPA Hyperprep mRNA (Supported Only For Legacy Projects) ===
The most common RNA kit option. Best for standard expression analysis. Includes polyA selection of mRNA. Data is strand-specific. 100-500ng total RNA.

=== KAPA Hyperprep with Ribo-depletion (Supported Only For Legacy Projects) ===
Instead of polyA selection of mRNA this kit specifically removes ribosomal RNA leaving behind mRNA and long non-coding RNA. Best for whole transcriptome (polyA and other transcripts) analysis. Data is strand-specific. 100-1000ng total RNA (more is better)

=== Clonetech SMART-Seq v4 Ultra-low (Supported Only For Legacy Projects) ===
For very low input RNA down to single cell. Data is NOT strand-specific. 10pg-10ng total RNA.

=== Clonetech SMARTer PICO (Supported Only For Legacy Projects) ===
For low input of degraded RNA. Data is strand-specific. 10-100ng total RNA.

=== NEBnext small RNA ===
For microRNA and other small RNA. 100-1000ng total RNA.

== DNA ==

=== Nextera gDNA ===
“Tagmentation” protocol for genomic or other DNA. Good for genomic DNA, ATAC-seq and other higher input DNA applications.

== Frequently Asked Questions ==
Please refer to [[Faq#Bulk_RNA-Seq|frequently asked questions section for FAQ regarding]] library prep options.

Sequencing

2024-07-10T21:51:12Z

Sgupta:

= TECHNOLOGY =

The GTC offers Next-Generation sequencing on the Illumina's NovaSeq and Element Bioscience's AVITI platform. More details on the [[Pricing| pricing]] page.

We also have Nanopore PS2 solo for long read sequencing.

= LIBRARY PREP SERVICE =

We offer many options for library prep for a wide range of applications and input levels down to RNA from single cells. Please refer to the pricing page for more information.

= PRICING =

For pricing information - [[Pricing| Click Here]]

{{SeqSubmissionGuide}}

= DATA =

Images acquired from the sequencer are processed through the bundled Illumina image extraction pipeline to get the sequence and quality score for each base. An in-depth QC report is included in the package.

* QC Details - [[SequencingQC|Sequencing]]
* Formats Details - [[SequencingFormats|Sequencing]]

== TURNAROUND TIME ==

2-3 weeks

= APPLICATIONS =

Next-Generation Sequencing can be used for a wide variety of applications including ChIP-Seq, RNA-Seq, smallRNA-seq, GWAS and much more. Visit Illumina's web site or contact us to discuss your project goals.

Sequencing

2024-07-10T21:50:56Z

Sgupta:

{{TopRightSideBar|
|title=Sequencing Service
|image=Dna_seq.jpg
|subtitle=
|highlights=

}}

= TECHNOLOGY =

The GTC offers Next-Generation sequencing on the Illumina's NovaSeq and Element Bioscience's AVITI platform. More details on the [[Pricing| pricing]] page.

We also have Nanopore PS2 solo for long read sequencing.

= LIBRARY PREP SERVICE =

We offer many options for library prep for a wide range of applications and input levels down to RNA from single cells. Please refer to the pricing page for more information.

= PRICING =

For pricing information - [[Pricing| Click Here]]

{{SeqSubmissionGuide}}

= DATA =

Images acquired from the sequencer are processed through the bundled Illumina image extraction pipeline to get the sequence and quality score for each base. An in-depth QC report is included in the package.

* QC Details - [[SequencingQC|Sequencing]]
* Formats Details - [[SequencingFormats|Sequencing]]

== TURNAROUND TIME ==

2-3 weeks

= APPLICATIONS =

Next-Generation Sequencing can be used for a wide variety of applications including ChIP-Seq, RNA-Seq, smallRNA-seq, GWAS and much more. Visit Illumina's web site or contact us to discuss your project goals.