imported>Stuart S. Levine: Created page with "== SEQUENCING == Please note that samples submitted from '''CORE LAB'''s will be given priority on all equipment. The BioMicro Center reserves the..."

2019-07-01T11:14:28Z

Created page with "== SEQUENCING == Please note that samples submitted from '''CORE LAB'''s will be given priority on all equipment. The BioMicro Center reserves the..."

New page

== SEQUENCING ==
Please note that samples submitted from [[BioMicroCenter:CoreDeps|'''CORE LAB''']]s will be given priority on all equipment. The BioMicro Center reserves the right to reject samples for any reason. 

=== HISEQ2000 SEQUENCING ===
{| class="wikitable" border=1
! HISEQ SEQUENCING
!width=80| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
!width=80| unit
! Notes
|-
|Single End 40nt
|align="right"| $1,200
|align="right"| $1,320
|align="right"| $1,800
|align="center"| per lane
| Includes final pool quality control (RT-PCR and BioAnalyzer), sequencing, genome alignment and data storage of BAM files for 1y.
|-
| Other read lengths
|colspan="5" align=left |7/1/18: Custom only. Requires purchase of full flowcell.
|}

=== NEXTSEQ500 SEQUENCING ===
{| class="wikitable" border=1
! NEXTSEQ SEQUENCING
!width=80| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
!width=80| unit
! Notes
|-
|91nt kit (eg. 40PE or 75SE)
|align="right"| $2,100
|align="right"| $2,320
|align="right"| $3,150
|align="center" rowspan="3"| per flowcell
|rowspan="3"| Includes final pool quality control (RT-PCR and BioAnalyzer), sequencing, genome alignment and data storage of BAM files for 1 year
|-
|166nt kit (eg. 80PE or 150SE)
|align="right"| $3,200
|align="right"| $3,520
|align="right"| $4,800
|-
|316nt kit (eg. 150PE or 300SE)
|align="right"| $4,900
|align="right"| $5,390
|align="right"| $7,350
|}

=== MISEQ SEQUENCING ===
{| class="wikitable" border=1
! MISEQ SEQUENCING
!width=80| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
!width=80| unit
! Notes
|-
|70nt V2 kit (eg. 30PE or 70SE)
|align="right"| $1,155
|align="right"| $1,270
|align="right"| $1,732
|align="center" rowspan=6| per lane
|rowspan=6| Includes final pool quality control (RT-PCR and BioAnalyzer), sequencing, genome alignment and data storage of BAM files for 1 year
|-
|150nt V3 kits (eg. 75PE)
|align="right"| $1,250
|align="right"| $1,375
|align="right"| $1,875
|-
|300nt V2 kit (eg. 150PE)
|align="right"| $1,365
|align="right"| $1,500
|align="right"| $2,050
|-
|500nt V2 kit (eg. 250PE)
|align="right"| $1,575
|align="right"| $1,732
|align="right"| $2,362
|-
| 600nt V3 kit (eg. 300PE)
|align="right"| $1,890
|align="right"| $2,080
|align="right"| $2,835
|-
| 500nt '''NANO''' Run (eg. 250PE)
|align="right"| $675
|align="right"| $742.50
|align="right"| $1,012.50
|}

=== OTHER ILLUMINA SERVICES ===
{| class="wikitable" border=1
! ILLUMINA SUPPORTING SERVICES
!width=80| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
!width=80| unit
! Notes
|-
| Quality Control Only -only one QC is included per sequencing lane.
|align="right"| $20
|align="right"| $26
|align="right"| $30
|align="center"| per sample
| Includes RT-PCR and Frag.Analyzer
|-
| Rapid Quality Control - Use SYBR for sample quantification for pooling instead of qPCR. Only available for pooling.
|align="right"| $10
|align="right"| $13
|align="right"| $15
|align="center"| per sample
| Includes Fluorometric quantification and Frag.Analyzer
|}

=== PACBIO SEQUENCING ===

{| class="wikitable" border=1
! SEQUEL SEQUENCING
!width=80| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
!width=80| unit
! Notes
|-
| 10 hour v3 Chemistry
|align="right"| $1,275
|align="right"| $1,405
|align="right"| $1,915
|align="center" rowspan=2| per SMRTCell
|rowspan=2| Includes polymerase binding and movie.
|-
| 20 hour v3 Chemistry
|align="right"| $1,400
|align="right"| $1,540
|align="right"| $2,100
|}

== LIBRARY GENERATION ==
=== ILLUMINA LIBRARY - DNA ===

{| class="wikitable" border=1
! ILLUMINA Sample Preparation
!width=120| Batch Size
!width=80| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
! Notes
|-
! colspan="3" | '''STANDARD THROUGHPUT DNA''' Prices for individual samples. Repreps will typically be attempted on failed samples without charge.
! colspan="3" style="color: blue;" | '''HIGH THROUGHPUT DNA''' Prices for sample batches. Repreps will NOT be attempted on failed samples without charge. Low volume (<=5ul) submission must be coordinated with BMC staff. Initial QC not included.
|-
|rowspan=3 |Standard Illumina Library (LM-PCR) NEB UltraII
|align="center"| per sample
|align="right"| $100
|align="right"| $110
|align="right"| $150
| Includes QC, adapter ligation, size selection, barcoding, enrichment, and quality control (SYBR and FA).
|- style="color: blue;"
|align="center"| 24 samples
|align="right"| $750
|align="right"| $825
|align="right"| $1075
|rowspan=2 | Includes adapter ligation, size selection, barcoding, enrichment, and quality control spotcheck (SYBR and FA).
|- style="color: blue;"
|align="center"| 96 samples
|align="right"| $1500
|align="right"| $1650
|align="right"| $2250
|-
| rowspan="4" | Tagmentation (NEXTERA-XT) - 1ng input
|align="center"| ''1'' Sample
|align="right"| $100
|align="right"| $110
|align="right"| $150
| rowspan="4" | Includes tagmentation, indexing, enrichment, and quality control (SYBR and FA).
|- style="color: blue;"
|align="center"| ''16'' (2 column) TECAN
|align="right" | $1000
|align="right" | $1100
|align="right" | $1500
|-
|align="center" style="color: blue;" | ''96'' Mosquito
|align="right" style="color: blue;" | $1500
|align="right" style="color: blue;" | $1650
|align="right" style="color: blue;" | $2250
|-
|align="center" style="color: blue;" | ''384'' Mosquito
|align="right" style="color: blue;" | $3000
|align="right" style="color: blue;" | $3300
|align="right" style="color: blue;" | $4500
|-
|rowspan="2" style="color: blue;" | 16S Amplicon
|align="center"|48 samples (6 columns)
|align="right" style="color: blue;" | $1,800
|align="right" style="color: blue;" | $1,980
|align="right" style="color: blue;" | $2,700
|rowspan="2" style="color: blue;" | Includes normalization, enrichment, pooling and quality control (SYBR and FA).
|-
|align="center"|add'l 48 samples (6 columns)
|align="right" style="color: blue;" | $600
|align="right" style="color: blue;" | $660
|align="right" style="color: blue;" | $900
|-
|rowspan="2" style="color: blue;" | Other Amplicon
|align="center" style="color: blue;" |48 samples (6 columns)
|align="right" style="color: blue;" | $1,440
|align="right" style="color: blue;" | $1,584
|align="right" style="color: blue;" | $2,160
|rowspan="2" style="color: blue;" | Includes normalization, enrichment, pooling and quality control (SYBR and FA). Samples *must* be submitted amplified with appropriate linkers.
|-
|align="center"|add'l 48 samples (6 columns)
|align="right" style="color: blue;" | $600
|align="right" style="color: blue;" | $660
|align="right" style="color: blue;" | $900
|-
! colspan="6" | '''ADDITIONAL FEES''' Samples not in proper input format will be subject to these additional charges.
|-
|style="color: blue;" | High Throughput Setup
|align="center" style="color: blue;" |48 samples
|align="right" style="color: blue;" | $50
|align="right" style="color: blue;" | $55
|align="right" style="color: blue;" | $75
|
|-
|Sample Cleanup
|align="center"|per sample
|align="right"| $5
|align="right"| $5.5
|align="right"| $7.5
|SPRI cleanup of samples to remove impurities.
|-
|style="color: blue;" |Quantification
|align="center" style="color: blue;" |per sample
|align="right" style="color: blue;" | $5
|align="right" style="color: blue;" | $5.5
|align="right" style="color: blue;" | $7.5
|Quantification of samples (FA) prior to arraying.
|}

=== ILLUMINA LIBRARY - RNA ===

{| class="wikitable" border=1
! ILLUMINA Sample Preparation
!width=120| Batch Size
!width=80| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
! Notes
|-
! colspan="3" | '''STANDARD RNA''' Prices for individual samples. Repreps will typically be attempted on failed samples without charge.
! colspan="3" style="color: blue;" | '''HIGH THROUGHPUT RNA''' Repreps will NOT be attempted on failed samples without charge. Low volume (<=5ul) submission must be coordinated with BMC staff. Initial QC not included
|-
|rowspan="2" | Standard polyA based isolation Kapa mRNA Hyperprep
|align="center"| per sample
|align="right"| $150
|align="right"| $165
|align="right"| $225
|Includes QC, polyA isolation, generation of cDNA, library construction, indexing and quality control (SYBR + FA).
|-
|align="center" style="color: blue;" | ''24'' TECAN
|align="right" style="color: blue;" | $2000
|align="right" style="color: blue;" | $2200
|align="right" style="color: blue;" | $3000
|Includes polyA isolation, generation of cDNA, library construction, indexing and quality control (SYBR + FA).
|-
| rowspan="2" style="color: blue;" | High Throughput 3' Digital Gene Expression (HT3DGE)
|align="center" style="color: blue;"| ''24'' TECAN
|align="right" style="color: blue;" | $1000
|align="right" style="color: blue;" | $1100
|align="right" style="color: blue;" | $1500
| rowspan="2" style="color: blue;" | Includes generation of cDNA, library construction, indexing and library quality control. Does not include sample QC.
|-
|align="center" style="color: blue;" | ''96'' TECAN
|align="right" style="color: blue;" | $4000
|align="right" style="color: blue;" | $4400
|align="right" style="color: blue;" | $6000
|-
|Total RNA sequencing:Mammalian Kapa Hyperprep + RiboErase
|align="center"| per sample
|align="right"| $225
|align="right"| $247.5
|align="right"| $337.5
|rowspan=2| Includes sample QC, ribosomal depletion, generation of cDNA, library construction, indexing and library quality control.
|-
|Total RNA sequencing:Other Kapa mRNA Hyperprep + Illumina RiboZero
|align="center"| per sample
|align="right"| $250
|align="right"| $275
|align="right"| $375
|-
|Low Input polyA+ Clontech SMARTseq v4 + NexteraXT
|align="center"| ''1'' sample
|align="right"| $250
|align="right"| $275
|align="right"| $375
| rowspan="3" | Includes generation of cDNA, amplification, library construction, indexing and quality control (SYBR + FA). Single sample includes initial QC.
|-
|rowspan="2"| Low Input polyA+ SMARTseq v2 + NexteraXT
|align="center" style="color: blue;" | ''24'' Mosquito
|align="right" style="color: blue;" | $1600
|align="right" style="color: blue;" | $1760
|align="right" style="color: blue;" | $2400
|-
|align="center" style="color: blue;" | ''96'' Mosquito
|align="right" style="color: blue;" | $2500
|align="right" style="color: blue;" | $2750
|align="right" style="color: blue;" | $3750
|-
|Low Input Mammalian Total Clontech ZapR Kit
|align="center"| ''1'' sample
|align="right"| $200
|align="right"| $220
|align="right"| $300
| rowspan="1" | Includes generation of cDNA, amplification, library construction, rRNA degradation, indexing and quality control (SYBR + FA).
|-
| Tight Size Cut
|align="center"| per pool
|align="right"| $85
|align="right"| $94
|align="right"| $130
| +/- 40bp using PippinPrep
|-
| Small RNA
| align="center"|per sample
| align="right"|$275
| align="right"|$303
| align="right"|$413
| Uses NEB, BIOO or QIAGEN small RNA kit
|-
! colspan="6" | '''ADDITIONAL FEES''' Samples not in proper input format will be subject to these additional charges.
|-
|style="color: blue;" | High Throughput Setup
|align="center" style="color: blue;" |48 samples
|align="right" style="color: blue;" | $50
|align="right" style="color: blue;" | $55
|align="right" style="color: blue;" | $75
|
|-
|Sample Cleanup
|align="center"|per sample
|align="right"| $5
|align="right"| $5.5
|align="right"| $7.5
|SPRI cleanup of samples to remove impurities.
|-
|style="color: blue;" |Quantification
|align="center" style="color: blue;" |12 samples
|align="right" style="color: blue;" | $5
|align="right" style="color: blue;" | $5.5
|align="right" style="color: blue;" | $7.5
|Quantification of samples (FA) prior to arraying.
|-
|}

.

=== PACBIO LIBRARIES ===
{| class="wikitable" border=1
! PacBio Sample Preparation
!width=120| Batch Size
!width=80| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
! Notes
|-
|rowspan=2|SMRTBell Only eg:PCR products
| Sample 1 || $300 || $330 || $450
|rowspan=2| Includes QC, repair and addition of indexed SMRTBells
|-
| Samples 2-8 || $150 || $165 || $225
|-
|rowspan=2|Genomic Library
| Sample 1 || $450 || $495 || $675
|rowspan=2| Includes Covaris gSPIN fragmentation, Pippin sizing, repair and SMRTbell as above
|-
| Sample 2-8 || $225 || $250 || $340
|}

== SINGLE CELL SERVICES ==
=== SEQWELL ===
{| class="wikitable" border=1
! 10X USAGE
!width=120| Batch Size
!width=80|KI
!width=80| [[BioMicroCenter:CoreDeps|OTHER CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
! Notes
|-
|colspan=7 align="center"|'''Assisted Service'''
|-
|FULL SERVICE Begin with cells
|per array|| - || - || - || - || Includes all steps, QC of cDNA Begins in KI Nanowell Core
|-
|FROM cDNA on BEADS
|per sample || $350 || $350 || $385 || $525
| Includes exonuclease treatment, amplification, QC of cDNA and library production Must coordinate with BMC staff on submission.
|-
|FROM AMPLIFIED cDNA
|per sample || $100 || $100 || $110 || $150 || Includes QC of cDNA and library production only.
|-
|colspan=7 align="center"|'''Reagents for SeqWell'''
|-
|SeqWell Array
|colspan=6 rowspan="2" | contact shanu@mit.edu for pricing and availability
|-
|SeqWell beads
|}

=== 10X CHROMIUM ===
{| class="wikitable" border=1
! 10X USAGE
!width=120| Batch Size
!width=80| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
! Notes
|-
|colspan=6 align="center"|'''Assisted Service'''
|-
|3'RNA (v3)|| per sample|| $1800 || $1980 || $2700 || Includes QC of cDNA and creation of Illumina Library
|-
|colspan=6 align="center"|'''Walk-up Service'''
|-
|3'RNA Beads and Reagents (v3)|| per samples || $1350 || $1485 || $2025 ||
|-
|ATACseq Beads and Reagents* || per sample || $1280 || $1408 || $1920 ||
|-
|scCNV Beads and Reagents* || per 4 samples || $1330 || $1463 || $1995 ||
|-
|Chips (up to 8 sample) || per chip || $350 || $385 || $525 || Includes service contract charge.
|-
|Training Limited to 2 people
|per method & per session Reagents not included || $500 || $550 || $750 ||
|}
*please let BMC know if you plan to run this method early so we will have reagents ready for you.

=== NAMOCELL ===
{| class="wikitable" border=1
! NAMOCELL
!width=120| Batch Size
!width=80| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=80| MIT
!width=80| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
! Notes
|-
|Cartridge|| 1 cartridge per sample|| $75 || $85 || $125 || Includes service contract charge
|}

== OTHER GENOMICS SERVICES ==

 

=== [[BioMicroCenter:QC|QUALITY CONTROL]] ===
{| class="wikitable" border=1
! QUALITY CONTROL
!width=100| unit
!width=100| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=100| MIT
!width=100| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
! Notes
|-
|Fragment Analyzer: RNA or DNA
|per sample ||$8 || $9 || $12
|
|-
|Fragment Analyzer: Preloaded row
| per row (12) ||$30 ||$33 || $45
| 2ul per sample in each well using plates from BMC
|-
|FemtoPulse: RNA or DNA
|per sample || $10 || $11 || $15
|
|-
|FemtoPulse: Preloaded Row
|per row (12) || $50 || $55 || $75
| 2ul per sample in each well using plates from BMC
|-
|BioAnalyzer: Assisted Service (RNA or DNA)
|per sample || $15 || $18 || $25
|
|-
|BioAnalyzer: Assisted Service (High Sensitivity protein)
|per sample || $40 || $44 || $60
| detection of proteins at < 30ng/ul.
|-
|}

=== [[BioMicroCenter:MicroArrays|MICROARRAYS]] ===

{| class="wikitable" border=1
! MICROARRAYS
!width=100| unit
!width=100| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=100| MIT
!width=100| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
! Notes
|-
| AGILENT SCANNER
|align="center"| per slide
|align="right"| $50
|align="right"| $50
|align="right"| N/A
| Price per glass slide.
|-
|}
Agilent scanning services will end 6/30/2019
 .

== [[BioMicroCenter:RTPCR|REAL TIME PCR]] ==

{| border=1
! OTHER LAB SERVICES
!width=100| [[BioMicroCenter:CoreDeps|CORE LAB / MIT]]
!width=100| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
!width=100| unit
! SIGN UP
! Notes
|-
| Roche LightCycler 480
|align="right"| $10
|align="right"| N/A
|align="center"| per plate
| [[BioMicroCenter:Forms#Calenders|CALENDAR]] *available for CORE only
| Contact [[BioMicroCenter:People|Noelani Kamelamela]] for training
|-
| SYBR Green (KAPA/Roche)
|align="right"| $25
|align="right"| N/A
|align="center"| per ml
|
| Available for MIT only
|-
| 96-well PLATES
|align="right"| $6
|align="right"| N/A
|align="center"| per plate
|
| Available for MIT only
|-
|}
.
 

== OTHER LAB SERVICES ==

{| border=1
! OTHER LAB SERVICES
!width=100| [[BioMicroCenter:CoreDeps|CORE LAB / MIT]]
!width=100| [[BioMicroCenter:FAQ#NON_MIT_USERS|Non-MIT]]
!width=100| unit
! SIGN UP
! Notes
|-
|colspan=6 align="center"| '''COVARIS SONICATOR'''
|-
|COVARIS E220
|align="right"|$20
|align="right"|$30
|per hour
|[https://mit.ilabsolutions.com/equipment/261752/?tab=schedule ilab calendar]
|tubes available for purchase.
|-
| colspan="6" align="center"| '''PIPPIN PREP'''
|-
|Gel Isolation
|align="right"| $50
|align="right"| $75
|align="center"| per gel (5 lanes)
| TBA
|
|-
|Training
|align="right"| $25
|align="right"| $50
|align="center"| per session
| TBA
| Contact [[BioMicroCenter:People|Noelani Kamelamela]] for training.
|-
| colspan="6" align="center"| '''PLATE READER'''
|-
| Varioskan
|align="right"| $18
|align="right"| $27
|align="center"| per hour
| [[BioMicroCenter:Forms#Calenders|CALENDAR]]
| Contact [[BioMicroCenter:People|Noelani Kamelamela]] for training
|-
| colspan="6" align="center"| '''ROBOTICS'''
|-
| Tecan EVO 150
|align="right"| $50
|align="right"| $55
|align="center"| per 1h block - based on scheduled time.
| [[BioMicroCenter:Forms#Calenders|CALENDAR]]
|
|-
|non-filter tips
|align="right"| $6.00
|align="right"| $6.00
|align="center"| per box
|
|** Please let us know if there is additional plasticware you would like us to stock.
|-
|Filter tips
|align="right"| $8.00
|align="right"| $8.00
|align="center"| per box
|
|
|-
| Training
|align="right"| $50
|align="right"| $55
|align="center"| per session
| Contact [[BioMicroCenter:People|Stuart]]
|
|-
| colspan="6" align="center"| '''NANODROP'''
|-
| Nanodrop
|align="right"| --
|align="right"| --
|align="center"|
| Walk up service
| * no charge
|-
|}
 

== COMPUTATIONAL SERVICES ==
{| class="wikitable" border=1
! COMPUTATIONAL SERVICES
!width=200| unit
!width=100| [[BioMicroCenter:CoreDeps|CORE LAB]]
!width=100| Other MIT / non-MIT
! Notes
|-
| Informatics Support
| align="right"| per hour
| align="right"| $80
| align="right"| $110 / $150
| Very limited support for non-MIT users
|-
| Informatics Share
| align="right"| per 0.1FTE
| align="right"| $1,100
| align="right"| N/A
| MIT only. Priority access to informatics.
|-
|Active Data storage
|align="right"| per TB per year
|align="right"| $160
|align="right"| $240 / N/A
|
|-
| Archival Storage (read only. Unmutable)
|align="right"| per TB per year
|align="right"| $80
|align="right"| $120 / N/A
|
|-
| Tape Archive / Recovery
|align="right"| per tape
|align="right"| $60
|align="right"| $70
|
|}

BioMicroCenter:PricingFY2019 - Revision history

imported>Stuart S. Levine: Created page with "== SEQUENCING == Please note that samples submitted from '''CORE LAB'''s will be given priority on all equipment. The BioMicro Center reserves the..."