Genome Technology Core (GTC) wiki - Sequencing and Microarray - User contributions [en]

RT PCR

2010-09-13T15:31:16Z

Jeongah:

The GTC features the 7900HT Fast Real-Time PCR system from Applied Biosystems for quantitative PCR. This highly flexible system supports both 96 and 384 well plate formats as well as the TLDA (TaqMan Low Density Array) card format. 

[https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=601255| Information about the 7900HT] 
[https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600694| Information about the TLDA system can be found here] 

== Access and Availability ==

The GTC has two ABI7900HT systems. One is set up for 384 well plates, the other for 96 well plates.

Access is available in 2 hour time blocks 24 hours a day, 7 days a week. Advance sign-up is required. It is recommended that you sign up at least 48 hours in advance to ensure availability. 

New users should contact Jeong-Ah Kwon [jkwon at wi dot mit dot edu] to schedule an orientation session.
Please do not attempt to change the blocks unless you have been trained as improper handling can damage the blocks. Jeong-Ah is available during normal business hours for training and consultation. 

Due to high demand, access to this equipment is limited to Whitehead Institute users only. 

==Sign-up policy==

We use a online sign-up system for the ABI 7900 machines. '''Please Carefully Read The Following Before You Book A Slot''' 

* Reserved Slots/Blocks cannot be deleted AFTER the timeslot begins. 
* All Reserved Slots/Blocks will be charged (unless deleted from the system). 
* Overbooking will not be tolerated. If you are identified as someone reserving more slots than you need and then deleting them, you will be penalized for misusing the system and creating inconvenience for others. 
* Please ensure you complete your run within your allotted timeslots/blocks. 
* Logging reagent usage is mandatory for everyone using the machines. If no GTC reagents are used, please log the number of plates and uLmix as 0) 
* You will get multiple email reminders to log your reagent usage If reagent usage is not logged by the 10th of the following month we will bill for the maximum potential usage.
 
You can sign-up for the a time slot to use the machine online. [[Calendar|Click Here For Details]].
 

The following consumables and reagents are available from the GTC for a fee:
* Optical plates (96-well fast, 384-well)
* Optical Adhesive Films
* TaqMan Universal Master Mix
* SYBR Green Master Mix

== Analysis ==

The analysis software SDS v2.3 is installed on our analysis computer located in room 352.

The installation disc is no longer available. You may download '''SDS software v2.4''' from [http://www.appliedbiosystems.com/absite/us/en/home/support/software/real-time-pcr/ab-7900ht.html here]

It is free and all you need is a serial number of the equipment. Please stop by for the number.

== Pricing ==
{{PricingHeader}}
{{PricingRow|SYBR green / Taq Man Master mix|uL|6.5 cents|-}}
{{PricingRow|Optical Plate|Plate|$7.00|-}}
{{PricingLastRow|Equipment Time (2 hour time block)|Plate|$30.00|Sign-up Required}}

RT PCR

2010-05-12T20:36:55Z

Jeongah: /* Access and Availability */

The GTC features the 7900HT Fast Real-Time PCR system from Applied Biosystems for quantitative PCR. This highly flexible system supports both 96 and 384 well plate formats as well as the TLDA (TaqMan Low Density Array) card format. 

[https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=601255| Information about the 7900HT] 
[https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600694| Information about the TLDA system can be found here] 

== Access and Availability ==

Access to the 7900HT is available in 2 hour time blocks 24 hours a day, 7 days a week. Advance sign-up is required. It is recommended that you sign up at least 48 hours in advance to ensure availability. 

New users should contact Jeong-Ah Kwon [jkwon at wi dot mit dot edu] to schedule an orientation session.
Please do not attempt to change the blocks unless you have been trained as improper handling can damage the blocks. Jeong-Ah is available during normal business hours for training and consultation. 

Due to high demand, access to this equipment is limited to Whitehead Institute users only. 

==Sign-up policy==

We use a online sign-up system for the ABI 7900 machines. '''Please Carefully Read The Following Before You Book A Slot''' 

* Reserved Slots/Blocks cannot be deleted AFTER the timeslot begins. 
* All Reserved Slots/Blocks will be charged (unless deleted from the system). 
* Overbooking will not be tolerated. If you are identified as some one reserving a lot more slots than you need and then deleting them, you will be penalized for misusing the system and creating inconvenience for others. 
* Please ensure you complete your run within your alloted timeslots/blocks. 
* Logging Reagent usage is mandatory for everyone using the machines. (It helps us send you reminders if you forget to log the reagents) 
* If no GTC reagents are used, please log the number of plates and uLmix as 0. 
* You will get multiple email reminders to log your reagent usage, if reagent usage is not logged by the 10th of the following Month. If you ignore those emails, we will bill for the maximum potential usage.
 
You can sign-up for the a time slot to use the machine online. [[Calendar|Click Here For Details]].
 

The following consumables and reagents are available from the GTC for a fee:
* Optical plates (96-well fast, 384-well)
* Optical Adhesive Films
* TaqMan Universal Master Mix
* SYBR Green Master Mix

== Analysis ==

The analysis software SDS v2.3 is installed on our analysis computer located in room 352. An installation disc is also available if you wish to work on your own computer (Windows XP only).

== Pricing ==
{{PricingHeader}}
{{PricingRow|SYBR green / Taq Man Master mix|uL|6.5 cents|-}}
{{PricingRow|Optical Plate|Plate|$7.00|-}}
{{PricingLastRow|Equipment Time (2 hour time block)|Plate|$30.00|Sign-up Required}}

RT PCR

2010-05-12T20:35:47Z

Jeongah:

The GTC features the 7900HT Fast Real-Time PCR system from Applied Biosystems for quantitative PCR. This highly flexible system supports both 96 and 384 well plate formats as well as the TLDA (TaqMan Low Density Array) card format. 

[https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=601255| Information about the 7900HT] 
[https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600694| Information about the TLDA system can be found here] 

== Access and Availability ==

Access to the 7900HT is available in 2 hour time blocks 24 hours a day, 7 days a week. Advance sign-up is required. It is recommended that you sign up at least 48 hours in advance to ensure availability. 

New users should contact Jeong-Ah Kwon [jkwon at wi dot mit dot edu] to schedule an orientation session. Current users who would like to learn how to change between 96 and 384 well plate blocks should also contact Jeong-Ah for training. Please do not attempt to change the blocks unless you have been trained as improper handling can damage the blocks. Jeong-Ah is available during normal business hours for training and consultation. 

Due to high demand, access to this equipment is limited to Whitehead Institute users only. 

==Sign-up policy==

We use a online sign-up system for the ABI 7900 machines. '''Please Carefully Read The Following Before You Book A Slot''' 

* Reserved Slots/Blocks cannot be deleted AFTER the timeslot begins. 
* All Reserved Slots/Blocks will be charged (unless deleted from the system). 
* Overbooking will not be tolerated. If you are identified as some one reserving a lot more slots than you need and then deleting them, you will be penalized for misusing the system and creating inconvenience for others. 
* Please ensure you complete your run within your alloted timeslots/blocks. 
* Logging Reagent usage is mandatory for everyone using the machines. (It helps us send you reminders if you forget to log the reagents) 
* If no GTC reagents are used, please log the number of plates and uLmix as 0. 
* You will get multiple email reminders to log your reagent usage, if reagent usage is not logged by the 10th of the following Month. If you ignore those emails, we will bill for the maximum potential usage.
 
You can sign-up for the a time slot to use the machine online. [[Calendar|Click Here For Details]].
 

The following consumables and reagents are available from the GTC for a fee:
* Optical plates (96-well fast, 384-well)
* Optical Adhesive Films
* TaqMan Universal Master Mix
* SYBR Green Master Mix

== Analysis ==

The analysis software SDS v2.3 is installed on our analysis computer located in room 352. An installation disc is also available if you wish to work on your own computer (Windows XP only).

== Pricing ==
{{PricingHeader}}
{{PricingRow|SYBR green / Taq Man Master mix|uL|6.5 cents|-}}
{{PricingRow|Optical Plate|Plate|$7.00|-}}
{{PricingLastRow|Equipment Time (2 hour time block)|Plate|$30.00|Sign-up Required}}

Pricing

2010-05-12T20:34:33Z

Jeongah:

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.

= Solexa Sequencing =

Sequencing pricing based on 7 samples per flow cell plus a control lane. Library preparation is not included in sequencing cost. Basic data analysis pipeline includes base calling and quality scores. Genome alignment and other analysis is available for an additional cost.
{{PricingHeader}}
{{PricingRow|Sequencing - 36 bp Single Read|Sample|~$850|Cluster, Sequence, Pipeline}}
{{PricingRow|Sequencing - 36 bp Paired-End Reads|Sample|~$1,500|Cluster, Sequence, Pipeline}}
{{PricingRow|Sample prep - ChIP Seq|Sample|Inquire|-}}
{{PricingRow|Sample prep - DGE|Sample|Inquire|-}}
{{PricingLastRow|Genome Alignment and other analysis|Sample|Inquire|-}}

 
 

= MicroArray Services =

Prices for sample processing do not include cost of arrays

== Affymetrix Array Processing==
{{PricingHeader}}
{{PricingRow|Affymetrix GeneChip Expression Array|Array|~$400|Array only}}
{{PricingRow|Standard Expression Processing|Sample|~$500|>5ug total RNA}}
{{PricingRow|Small Sample Expression Processing|Sample|~$650|10-100ng total RNA}}
{{PricingLastRow|Prokaryotic Protocol|Sample|~$450|-}}

 
== Agilent Array Processing==
{{PricingHeader}}
{{PricingRow|Agilent Expression Array 4x44k multiplex|"Slide (array)"|~$700/slide|($175/array)|"Arrays only 4 arrays per slide"}}
{{PricingRow|Standard Expression Processing|Sample|~$350|One sample, single channel}}
{{PricingLastRow|ChIP-on-Chip Processing|Sample|~$650|Two samples, dual channel}}

 

== Custom Array Manufacturing==
{{PricingHeader}}
{{PricingLastRow|Up to 30,000 spots on 100 slides||Inquire|-}}

 

= Bioanalyzer - RNA, DNA and Protein analysis =
{{PricingHeader}}
{{PricingLastRow|Bioanalyzer run|Run|$150|Up to 12 samples per run}}

 
= Quantitative PCR - ABI Prism 7900 =
{{PricingHeader}}
{{PricingRow|SYBR green / Taq Man Master mix|uL|6.5 cents|-}}
{{PricingRow|Optical Plate|Plate|$7.00|-}}
{{PricingLastRow|Equipment Time (2 hour time block)|Plate|$30.00|Sign-up Required}}

 
 
= Other Services =
 
== General Liquid Handling - Biomek FX ==
{{PricingHeader}}
{{PricingLastRow|96 Channel or single well hit-picking||Inquire|-}}

 

== Monthly Access Program ==
Regular users are encouraged to subscribe to our monthly access program that provides unlimited use of general equipment including the nanodrop spectrophotometer, hybridization chambers and ovens, pipettes and some common supplies. The fee is $250/month and covers the entire lab.

Forms

2009-05-19T19:32:06Z

Jeongah:

{{TopRightSideBar|
|title=Sample Submission Forms
|image=Forms.jpg
|subtitle=Sample Submission Forms
|highlights=

}}

=New Customer Form=
[http://jura.wi.mit.edu/cmtwiki/images/8/83/New_Cust_Bill_Frmv2.xls New Customer Form]

=Sequencing=
[http://jura.wi.mit.edu/genomecorewiki/images/c/c6/Solexa_Submission_Form_v4.xls Solexa Sample Submission Form] - Use this form for all solexa sample submissions.

[[Sequencing| Service Details...]]

=Microarray=

== Expression Analysis ==
[http://jura.wi.mit.edu/cmtwiki/images/a/aa/AffySubForm_v9.xls Affy Sample Submission Form]
 
[http://jura.wi.mit.edu/cmtwiki/images/4/4c/MicroarraySubForm_v8.xls Agilent Sample Submission Form]

[[Expression_Analysis_Services| Service Details...]]

== ChIP on Chip/Location Analysis ==
[http://jura.wi.mit.edu/cmtwiki/images/f/f7/GWLASubForm_v4.xls Agilent ChIP-CHIP Sample Submission Form]

[[ChIP_on_Chip| Service Details...]]

== [[MiRNA_Services| miRNA Analysis]] ==
[http://jura.wi.mit.edu/cmtwiki/images/d/d7/MiRNASubFormv1.xls Exiqon Sample Submission Form]

[[MiRNA_Services| Service Details...]]

=Other Services=

== Bioanalyzer/Sample QC ==
[http://jura.wi.mit.edu/genomecorewiki/images/4/45/QCSubForm_ForWeb.xls Bioanalyzer QC Sample Submission Form]

== RT PCR ==
[[RTPCRLog|Book RT-PCR Machine in Rm 325]]

[[RT_PCR| Service Details...]]

Forms

2009-05-19T19:31:13Z

Jeongah:

{{TopRightSideBar|
|title=Sample Submission Forms
|image=Forms.jpg
|subtitle=Sample Submission Forms
|highlights=

}}

=New Customer Form=
[http://jura.wi.mit.edu/cmtwiki/images/8/83/New_Cust_Bill_Frmv2.xls New Customer Form]

=Sequencing=
[http://jura.wi.mit.edu/genomecorewiki/images/3/31/Solexa_Submission_Form_v4.xls Solexa Sample Submission Form] - Use this form for all solexa sample submissions.

[[Sequencing| Service Details...]]

=Microarray=

== Expression Analysis ==
[http://jura.wi.mit.edu/cmtwiki/images/a/aa/AffySubForm_v9.xls Affy Sample Submission Form]
 
[http://jura.wi.mit.edu/cmtwiki/images/4/4c/MicroarraySubForm_v8.xls Agilent Sample Submission Form]

[[Expression_Analysis_Services| Service Details...]]

== ChIP on Chip/Location Analysis ==
[http://jura.wi.mit.edu/cmtwiki/images/f/f7/GWLASubForm_v4.xls Agilent ChIP-CHIP Sample Submission Form]

[[ChIP_on_Chip| Service Details...]]

== [[MiRNA_Services| miRNA Analysis]] ==
[http://jura.wi.mit.edu/cmtwiki/images/d/d7/MiRNASubFormv1.xls Exiqon Sample Submission Form]

[[MiRNA_Services| Service Details...]]

=Other Services=

== Bioanalyzer/Sample QC ==
[http://jura.wi.mit.edu/genomecorewiki/images/4/45/QCSubForm_ForWeb.xls Bioanalyzer QC Sample Submission Form]

== RT PCR ==
[[RTPCRLog|Book RT-PCR Machine in Rm 325]]

[[RT_PCR| Service Details...]]

File:Solexa Submission Form v4.xls

2009-05-19T19:25:36Z

Jeongah: update on sample submission 051909

update on sample submission 051909

Forms

2009-05-12T20:02:03Z

Jeongah:

{{TopRightSideBar|
|title=Sample Submission Forms
|image=Forms.jpg
|subtitle=Sample Submission Forms
|highlights=

}}

=New Customer Form=
[http://jura.wi.mit.edu/cmtwiki/images/8/83/New_Cust_Bill_Frmv2.xls New Customer Form]

=Sequencing=
[http://jura.wi.mit.edu/genomecorewiki/images/3/31/Solexa_Submission_Form_v3.xls Solexa Sample Submission Form] - Use this form for all solexa sample submissions.

[[Sequencing| Service Details...]]

=Microarray=

== Expression Analysis ==
[http://jura.wi.mit.edu/cmtwiki/images/a/aa/AffySubForm_v9.xls Affy Sample Submission Form]
 
[http://jura.wi.mit.edu/cmtwiki/images/4/4c/MicroarraySubForm_v8.xls Agilent Sample Submission Form]

[[Expression_Analysis_Services| Service Details...]]

== ChIP on Chip/Location Analysis ==
[http://jura.wi.mit.edu/cmtwiki/images/f/f7/GWLASubForm_v4.xls Agilent ChIP-CHIP Sample Submission Form]

[[ChIP_on_Chip| Service Details...]]

== [[MiRNA_Services| miRNA Analysis]] ==
[http://jura.wi.mit.edu/cmtwiki/images/d/d7/MiRNASubFormv1.xls Exiqon Sample Submission Form]

[[MiRNA_Services| Service Details...]]

=Other Services=

== Bioanalyzer/Sample QC ==
[http://jura.wi.mit.edu/genomecorewiki/images/4/45/QCSubForm_ForWeb.xls Bioanalyzer QC Sample Submission Form]

== RT PCR ==
[[RTPCRLog|Book RT-PCR Machine in Rm 325]]

[[RT_PCR| Service Details...]]

File:Solexa Submission Form v3.xls

2009-05-12T20:00:06Z

Jeongah: