Faq - Revision history

Sgupta at 18:58, 4 June 2020

2020-06-04T18:58:15Z

Sgupta at 16:12, 5 February 2020

2020-02-05T16:12:06Z

Sgupta at 15:44, 5 February 2020

2020-02-05T15:44:53Z

Sgupta: /* General */

2007-04-09T22:24:46Z

‎General

Sgupta at 16:59, 4 April 2007

2007-04-04T16:59:04Z

Sgupta at 16:51, 4 April 2007

2007-04-04T16:51:26Z

10.9.31.223 at 16:47, 4 April 2007

2007-04-04T16:47:11Z

10.9.31.223 at 16:40, 4 April 2007

2007-04-04T16:40:47Z

10.9.31.223 at 21:53, 3 April 2007

2007-04-03T21:53:48Z

10.9.31.223 at 21:49, 3 April 2007

2007-04-03T21:49:10Z

New page

questions

← Older revision		Revision as of 18:58, 4 June 2020
Line 92:		Line 92:
	=== What’s your shipping address? ===		=== What’s your shipping address? ===
	Please ship your materials to: Whitehead Institute Genome Technology Core, 455 Main Street, Room 325, Cambridge MA, 02145.		Please ship your materials to: Whitehead Institute Genome Technology Core, 455 Main Street, Room 325, Cambridge MA, 02145.
		+
		+
		+	== NGS Data Analysis For External Customers ==
		+	We can provide some analysis results using standardized methods along with the processed data. Please email a brief description of your analysis request to Sumeet Gupta (sgupta@wi.mit.edu) for review. Any additional charges would be communicated on a project by project basis.

@@ Line 27: / Line 27: @@
-== Library Prep ==
+== Sample Submission ==
-=== I just want standard RNA-seq data for expression analysis, which kit should I use? ===
+=== Where can I find the forms I need to submit samples? ===
 KAPA Hyperprep mRNA if you have more than 100ng of input RNA
-=== I have less than 100ng of input RNA, can I still use KAPA Hyperprep? ===
+==== I have less than 100ng of input RNA, can I still use KAPA Hyperprep? ====
 If the RNA is high quality, KAPA HyperPrep may work with less than 100ng but it is risky. A safer approach is to use 10ng in the Clonetech SMART-seq v4 Ultra-low kit.
-=== What’s the difference in the data between KAPA HyperPrep and Clonetech Ultralow? ===
+==== What’s the difference in the data between KAPA HyperPrep and Clonetech Ultralow? ====
 KAPA data is stranded and probably higher fidelity. The Clonetech Ultralow kit involves more amplification and that can lead to bias but for low input it is the best kit available.
-=== Can I compare data from different kits? ===
+==== Can I compare data from different kits? ====
 Kits with similar approaches from different companies will generally be comparable (e.g. KAPA HyperPrep, TruSeq mRNA and NEB Next Ultra II) HOWEVER additional processing/correction may be required. Care should be taken if trying to compare one of the “standard” kits to a low input kit like Clonetech UltraLow due to possible bias in the low input kit.

@@ Line 9: / Line 9: @@
 == General ==
-=== Which platforms do you support for expression analysis? ===
+=== How do I sign up to use your RT-PCR machine? ===
-We support Affymetrix, Agilent and printed arrays from Operon.
+To sign up for time, please see the calendar - http://genomecore.wi.mit.edu/index.php/Calendar.
-=== How do I sign up to use your ABI Prism 700 RT-PCR machine? ===
+=== Do you have bench/work space for visiting users in the WIGTC laboratory? What about tips, etc? ===
 WICMT has available bench space for visitors to use. We  supply tips and gloves. Please be aware that this bench space,  as well as WICMT refrigerators and freezers, is a “glove zone” –  please wear gloves when handling WICMT tips, reagents, etc.
@@ Line 24: / Line 21: @@
 Yes. We will ship your samples and leftover arrays back  to you. Please provide a FedEx number on your sample  submission form.
-=== How long does it take? ===
+== Pricing ==
-Please allow 2-4 weeks for completion of the entire analysis from receipt of samples to delivery of the final data.
+=== How much will my experiment cost? ===
-=== What about unused sample? ===
+=== What’s the difference in the data between KAPA HyperPrep and Clonetech Ultralow? ===
-== Pricing ==
+=== Can I compare data from different kits? ===
-=== How much does it cost to do a microarray experiment? ===
+Kits with similar approaches from different companies will generally be comparable (e.g. KAPA HyperPrep, TruSeq mRNA and NEB Next Ultra II) HOWEVER additional processing/correction may be required. Care should be taken if trying to compare one of the “standard” kits to a low input kit like Clonetech UltraLow due to possible bias in the low input kit.
 == Sample Submission ==
@@ Line 43: / Line 45: @@
 For the standard one-cycle labeling protocol we request 10ug  total RNA, and an extra 1ug for QC. For the small  sample (two-cycle) labeling protocol, 25-50ng total RNA is  requested. It is always beneficial to supply enough RNA for  two sample preps, if possible. This is just for security. One and two cycle labeling is available for all supported array platforms.
-=== How do I submit samples to WICMT for processing? ===
+=== Where can I find the forms I need to submit samples? ===
-Please download the Sample Submission Form  on the Forms page. There is no need to submit any secondary forms,  since this form provides your contact information, as well as  information about your samples.
+See our Forms page for all our submission forms - http://genomecore.wi.mit.edu/index.php/Forms
 == Shipping ==
-=== How do I ship my RNA to WICMT? ===
+=== How do I ship my RNA to WIGTC? ===
-If you are shipping within the U.S., please send your samples  by overnight priority shipping on dry ice. If you are shipping  internationally, please send your samples at room temperature,  precipitated in EtOH and NaOAc according to your lab  protocol. WICMT will chill your samples overnight to precipitate,  and then spin down and resuspend your RNA. In this case, it is imperative that you supply at least double the amount of RNA  you would normally supply.
+If you are shipping within the U.S., please send your samples  by overnight priority shipping on dry ice. If you are shipping  internationally, please send your samples at room temperature,  precipitated in EtOH and NaOAc according to your lab  protocol.
 === What’s your shipping address? ===
-Please ship your materials to: Jennifer Love, Whitehead Institute Center for Microarray Technology, 9 Cambridge Center, Room 325, Cambridge MA, 02145.
+Please ship your materials to: Whitehead Institute Genome Technology Core, 455 Main Street, Room 325, Cambridge MA, 02145.

@@ Line 25: / Line 25: @@
 === How long can I expect to wait for my project to be  completed? ===
 We pride ourselves on fast turnaround but our project list  can get quite long. At the time of sample submission we will  provide you with an estimate of when the project will be  completed. Expression analysis projects cannot be scheduled until RNA is submitted. Typical wait time for standard service projects is  about 2 weeks.
 == Pricing ==

@@ Line 9: / Line 9: @@
 == General ==
-Q: Which platforms do you support for expression analysis?
+=== Which platforms do you support for expression analysis? ===
-A: We support Affymetrix, Agilent and printed arrays from Operon.
+We support Affymetrix, Agilent and printed arrays from Operon.
 == Pricing ==
@@ Line 17: / Line 31: @@
 Please see the Pricing page for our full price list. Please  note that non-WI/MIT academic institutions should add 30%  to the list price. Commercial entities should add 60%. Contact us for  Affymetrix Gene Chip or Agilent catalog array pricing. Quotes are available for larger projects.   Q: How much does it cost to print a custom array? A: Pricing for custom array projects is a function of labor,  equipment time and supplies (slides). Every project is different  and it is often difficult to predict the total costs until the work  is complete. Customers interested in printing custom arrays  should contact Tom Volkert for estimates.    Q: Is there a bulk discount for processing large numbers of  samples? A: Volume discounts are available, contact WICMT for details.
 === How much RNA do I need to do a microarray experiment? ===
 For the standard one-cycle labeling protocol we request 10ug  total RNA, and an extra 1ug for QC. For the small  sample (two-cycle) labeling protocol, 25-50ng total RNA is  requested. It is always beneficial to supply enough RNA for  two sample preps, if possible. This is just for security. One and two cycle labeling is available for all supported array platforms.
@@ Line 26: / Line 44: @@
 See our Forms page for all our submission forms.
 === How do I ship my RNA to WICMT? ===
 If you are shipping within the U.S., please send your samples  by overnight priority shipping on dry ice. If you are shipping  internationally, please send your samples at room temperature,  precipitated in EtOH and NaOAc according to your lab  protocol. WICMT will chill your samples overnight to precipitate,  and then spin down and resuspend your RNA. In this case, it is imperative that you supply at least double the amount of RNA  you would normally supply.
 === How do I ship my Affymetrix Gene Chips to WICMT? ===
 You can ship the Gene Chips at room temperature by  overnight priority shipping. Once here, they will be stored in  our refrigerators. Please write your name on the boxes before  you send them.
 === How do I drop-ship Affymetrix Gene Chips to WICMT? ===
-A: Because WICMT is a service facility, we have made  arrangements with Affymetrix to allow our customers to order  and pay for Gene Chips themselves, and have the Gene Chips  shipped directly to our laboratory. Please be sure to mention  this arrangement when placing your order. Please have the  chips delivered in your name, care of Jennifer Love. This will  make keeping track of arriving chips more efficient. Please see  our shipping address above. WICMT cannot order chips for  customers outside of the Whitehead Institute or MIT.
+A: Because WICMT is a service facility, we have made  arrangements with Affymetrix to allow our customers to order  and pay for Gene Chips themselves, and have the Gene Chips  shipped directly to our laboratory. Please be sure to mention  this arrangement when placing your order. Please have the  chips delivered in your name, care of Jennifer Love. This will make keeping track of arriving chips more efficient. Please see  our shipping address above. WICMT cannot order chips for  customers outside of the Whitehead Institute or MIT.

@@ Line 12: / Line 12: @@
 A: We support Affymetrix, Agilent and printed arrays from Operon.
-Q: How much RNA do I need to do a microarray experiment?
+== Pricing ==
-A: For the standard one-cycle labeling protocol we request 10ug  total RNA, and an extra 1ug for QC. For the small  sample (two-cycle) labeling protocol, 25-50ng total RNA is  requested. It is always beneficial to supply enough RNA for  two sample preps, if possible. This is just for security. One and two cycle labeling is available for all supported array platforms.
+=== How much does it cost to do a microarray experiment? ===
-Q: How do I submit samples to WICMT for processing?
+=== How much RNA do I need to do a microarray experiment? ===
-A: Please download the Sample Submission Form  on the Forms page. There is no need to submit any secondary forms,  since this form provides your contact information, as well as  information about your samples.
+For the standard one-cycle labeling protocol we request 10ug  total RNA, and an extra 1ug for QC. For the small  sample (two-cycle) labeling protocol, 25-50ng total RNA is  requested. It is always beneficial to supply enough RNA for  two sample preps, if possible. This is just for security. One and two cycle labeling is available for all supported array platforms.
-Q: Where can I find the forms I need to submit samples?
+=== How do I submit samples to WICMT for processing? ===
-A: See our Forms page for all our submission forms.
+Please download the Sample Submission Form  on the Forms page. There is no need to submit any secondary forms,  since this form provides your contact information, as well as  information about your samples.
-Q: How do I ship my RNA to WICMT?
+=== Where can I find the forms I need to submit samples? ===
-A: If you are shipping within the U.S., please send your samples  by overnight priority shipping on dry ice. If you are shipping  internationally, please send your samples at room temperature,  precipitated in EtOH and NaOAc according to your lab  protocol. WICMT will chill your samples overnight to precipitate,  and then spin down and resuspend your RNA. In this case, it is imperative that you supply at least double the amount of RNA  you would normally supply.
+See our Forms page for all our submission forms.
-Q: How do I ship my Affymetrix Gene Chips to WICMT?
+=== How do I ship my RNA to WICMT? ===
-A: You can ship the Gene Chips at room temperature by  overnight priority shipping. Once here, they will be stored in  our refrigerators. Please write your name on the boxes before  you send them.
+If you are shipping within the U.S., please send your samples  by overnight priority shipping on dry ice. If you are shipping  internationally, please send your samples at room temperature,  precipitated in EtOH and NaOAc according to your lab  protocol. WICMT will chill your samples overnight to precipitate,  and then spin down and resuspend your RNA. In this case, it is imperative that you supply at least double the amount of RNA  you would normally supply.
-Q: How is my RNA checked for quality control before processing?
+=== How do I ship my Affymetrix Gene Chips to WICMT? ===
-A: We use Agilent’s Bioanalyzer 2100 for RNA QC. Please see  Agilent’s website for more information.
+You can ship the Gene Chips at room temperature by  overnight priority shipping. Once here, they will be stored in  our refrigerators. Please write your name on the boxes before  you send them.
-Q: Will I get my samples back after my experiment is complete?
+=== How is my RNA checked for quality control before processing? ===
-A: Yes. We will ship your samples and leftover arrays back  to you. Please provide a FedEx number on your sample  submission form.
+We use Agilent’s Bioanalyzer 2100 for RNA QC. Please see  Agilent’s website for more information.
-Q: How do I sign up for your monthly lab use program? How  much does it cost? What does it include?
+=== Will I get my samples back after my experiment is complete? ===
-A: The WICMT monthly lab use program is easy to sign up for  and use! A monthly fee of $250 covers your lab’s usage of  common equipment, such as the Nanodrop spectrophotometer  and the SpeedVac, and occasional usage of other equipment  as needed. Please note that this monthly lab use fee does NOT  include the ABI Prism 700 RT-PCR machine, Affymetrix  equipment, or the Biomek. To sign your lab up, contact  Jennifer Love with your request. You will begin receiving  monthly invoices from WICMT right away.
+Yes. We will ship your samples and leftover arrays back  to you. Please provide a FedEx number on your sample  submission form.
-Q: How long can I expect to wait for my project to be  completed?
+=== How do I enroll for your monthly lab use program? How much does it cost? What does it include? ===
-A: We pride ourselves on fast turnaround but our project list  can get quite long. At the time of sample submission we will  provide you with an estimate of when the project will be  completed. Expression analysis projects cannot be scheduled until RNA is submitted. Typical wait time for standard service projects is  about 2 weeks.
+The WICMT monthly lab use program is easy to sign up for and use! A monthly fee of $250 covers your lab’s usage of  common equipment, such as the Nanodrop spectrophotometer  and the SpeedVac, and occasional usage of other equipment  as needed. Please note that this monthly lab use fee does NOT  include the ABI Prism 700 RT-PCR machine, Affymetrix  equipment, or the Biomek. To sign your lab up, contact  Jennifer Love with your request. You will begin receiving  monthly invoices from WICMT right away.
-Q: How do I sign up to use your ABI Prism 700 RT-PCR machine?
+=== How long can I expect to wait for my project to be  completed? ===
-A: To sign up for time on the ABI Prism, please see the calendar  on the desk mat underneath the laptop which runs the  machine. Please note that there are time blocks, which are  explained in a note on the wall by the calendar. These time  blocks include only machine time. Please plan accordingly.
+We pride ourselves on fast turnaround but our project list  can get quite long. At the time of sample submission we will  provide you with an estimate of when the project will be  completed. Expression analysis projects cannot be scheduled until RNA is submitted. Typical wait time for standard service projects is  about 2 weeks.
-Q: Do you have bench/work space for visiting users in the  WICMT laboratory? What about tips, etc?
+=== How do I sign up to use your ABI Prism 700 RT-PCR machine? ===
-A: WICMT has available bench space for visitors to use. We  supply tips and gloves. Please be aware that this bench space,  as well as WICMT refrigerators and freezers, is a “glove zone” –  please wear gloves when handling WICMT tips, reagents, etc.
+To sign up for time on the ABI Prism, please see the calendar  on the desk mat underneath the laptop which runs the  machine. Please note that there are time blocks, which are  explained in a note on the wall by the calendar. These time  blocks include only machine time. Please plan accordingly.
-Q: What’s your shipping address?
+=== Do you have bench/work space for visiting users in the  WICMT laboratory? What about tips, etc? ===
-A: Please ship your materials to:
+WICMT has available bench space for visitors to use. We  supply tips and gloves. Please be aware that this bench space,  as well as WICMT refrigerators and freezers, is a “glove zone” –  please wear gloves when handling WICMT tips, reagents, etc.
-Q: How do I drop-ship Affymetrix Gene Chips to WICMT?
+=== How do I drop-ship Affymetrix Gene Chips to WICMT? ===
 A: Because WICMT is a service facility, we have made  arrangements with Affymetrix to allow our customers to order  and pay for Gene Chips themselves, and have the Gene Chips  shipped directly to our laboratory. Please be sure to mention  this arrangement when placing your order. Please have the  chips delivered in your name, care of Jennifer Love. This will  make keeping track of arriving chips more efficient. Please see  our shipping address above. WICMT cannot order chips for  customers outside of the Whitehead Institute or MIT.

← Older revision		Revision as of 16:47, 4 April 2007
Line 6:		Line 6:

	}}		}}
		+
		+	== General ==

	Q: Which platforms do you support for expression analysis?		Q: Which platforms do you support for expression analysis?

← Older revision		Revision as of 16:40, 4 April 2007
Line 7:		Line 7:
	}}		}}

−	~~questions~~	+	Q: Which platforms do you support for expression analysis?
		+	A: We support Affymetrix, Agilent and printed arrays from Operon.
		+
		+	Q: How much does it cost to do a microarray experiment? A: Please see the Pricing page for our full price list. Please note that non-WI/MIT academic institutions should add 30% to the list price. Commercial entities should add 60%. Contact us for Affymetrix Gene Chip or Agilent catalog array pricing. Quotes are available for larger projects. Q: How much does it cost to print a custom array? A: Pricing for custom array projects is a function of labor, equipment time and supplies (slides). Every project is different and it is often difficult to predict the total costs until the work is complete. Customers interested in printing custom arrays should contact Tom Volkert for estimates. Q: Is there a bulk discount for processing large numbers of samples? A: Volume discounts are available, contact WICMT for details.
		+
		+	Q: How much RNA do I need to do a microarray experiment?
		+	A: For the standard one-cycle labeling protocol we request 10ug total RNA, and an extra 1ug for QC. For the small sample (two-cycle) labeling protocol, 25-50ng total RNA is requested. It is always beneficial to supply enough RNA for two sample preps, if possible. This is just for security. One and two cycle labeling is available for all supported array platforms.
		+
		+	Q: How do I submit samples to WICMT for processing?
		+	A: Please download the Sample Submission Form on the Forms page. There is no need to submit any secondary forms, since this form provides your contact information, as well as information about your samples.
		+
		+	Q: Where can I find the forms I need to submit samples?
		+	A: See our Forms page for all our submission forms.
		+
		+	Q: How do I ship my RNA to WICMT?
		+	A: If you are shipping within the U.S., please send your samples by overnight priority shipping on dry ice. If you are shipping internationally, please send your samples at room temperature, precipitated in EtOH and NaOAc according to your lab protocol. WICMT will chill your samples overnight to precipitate, and then spin down and resuspend your RNA. In this case, it is imperative that you supply at least double the amount of RNA you would normally supply.
		+
		+	Q: How do I ship my Affymetrix Gene Chips to WICMT?
		+	A: You can ship the Gene Chips at room temperature by overnight priority shipping. Once here, they will be stored in our refrigerators. Please write your name on the boxes before you send them.
		+
		+	Q: How is my RNA checked for quality control before processing?
		+	A: We use Agilent’s Bioanalyzer 2100 for RNA QC. Please see Agilent’s website for more information.
		+
		+	Q: Will I get my samples back after my experiment is complete?
		+	A: Yes. We will ship your samples and leftover arrays back to you. Please provide a FedEx number on your sample submission form.
		+
		+	Q: How do I sign up for your monthly lab use program? How much does it cost? What does it include?
		+	A: The WICMT monthly lab use program is easy to sign up for and use! A monthly fee of $250 covers your lab’s usage of common equipment, such as the Nanodrop spectrophotometer and the SpeedVac, and occasional usage of other equipment as needed. Please note that this monthly lab use fee does NOT include the ABI Prism 700 RT-PCR machine, Affymetrix equipment, or the Biomek. To sign your lab up, contact Jennifer Love with your request. You will begin receiving monthly invoices from WICMT right away.
		+
		+	Q: How long can I expect to wait for my project to be completed?
		+	A: We pride ourselves on fast turnaround but our project list can get quite long. At the time of sample submission we will provide you with an estimate of when the project will be completed. Expression analysis projects cannot be scheduled until RNA is submitted. Typical wait time for standard service projects is about 2 weeks.
		+
		+	Q: How do I sign up to use your ABI Prism 700 RT-PCR machine?
		+	A: To sign up for time on the ABI Prism, please see the calendar on the desk mat underneath the laptop which runs the machine. Please note that there are time blocks, which are explained in a note on the wall by the calendar. These time blocks include only machine time. Please plan accordingly.
		+
		+	Q: Do you have bench/work space for visiting users in the WICMT laboratory? What about tips, etc?
		+	A: WICMT has available bench space for visitors to use. We supply tips and gloves. Please be aware that this bench space, as well as WICMT refrigerators and freezers, is a “glove zone” – please wear gloves when handling WICMT tips, reagents, etc.
		+
		+	Q: What’s your shipping address?
		+	A: Please ship your materials to:
		+	Jennifer Love
		+	Whitehead Institute Center for Microarray Technology
		+	9 Cambridge Center Room 325
		+	Cambridge MA, 02145
		+
		+	Q: How do I drop-ship Affymetrix Gene Chips to WICMT?
		+	A: Because WICMT is a service facility, we have made arrangements with Affymetrix to allow our customers to order and pay for Gene Chips themselves, and have the Gene Chips shipped directly to our laboratory. Please be sure to mention this arrangement when placing your order. Please have the chips delivered in your name, care of Jennifer Love. This will make keeping track of arriving chips more efficient. Please see our shipping address above. WICMT cannot order chips for customers outside of the Whitehead Institute or MIT.

← Older revision		Revision as of 21:53, 3 April 2007
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		+	\|title=FAQ's
		+	\|image=faq.jpg
		+	\|subtitle=Frequently Asked Questions
		+	\|highlights=
		+
		+	}}
		+
	questions		questions