BioMicroCenter:FAQ - Revision history

Scott J. Morin: /* Custom Primers */

2013-04-17T02:21:57Z

Custom Primers

←Older revision		Revision as of 02:21, 17 April 2013
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	When submitting [[BioMicroCenter:Sequencing\|'''custom primers''']], be sure to verify their compatibility with the standard Illumina Primers used. If you'd like a second opinion on the compatibility of your primers, we'd be more than happy to sit down with you and verify the primer design based on your constructs.		When submitting [[BioMicroCenter:Sequencing\|'''custom primers''']], be sure to verify their compatibility with the standard Illumina Primers used. If you'd like a second opinion on the compatibility of your primers, we'd be more than happy to sit down with you and verify the primer design based on your constructs.

-	Another important aspect to consider is the fact that clustering conditions differ when comparing the HiSeq to the MiSeq. The MiSeq clusters at about 5 degrees higher than the cBot, which is used to prepare flowcells for the HiSeq. This means that all custom primers must be designed appropriately so ~~there~~ Tm's are compatible with whatever sequencing route you choose.	+	Another important aspect to consider is the fact that clustering conditions differ when comparing the HiSeq to the MiSeq. The MiSeq clusters at about 5 degrees higher than the cBot, which is used to prepare flowcells for the HiSeq. This means that all custom primers must be designed appropriately so Tm's are compatible with whatever sequencing route you choose.

	== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==		== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==

Scott J. Morin: /* Custom Primers */

2013-04-17T02:20:59Z

Custom Primers

←Older revision		Revision as of 02:20, 17 April 2013
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	=== Custom Primers ===		=== Custom Primers ===
	When submitting [[BioMicroCenter:Sequencing\|'''custom primers''']], be sure to verify their compatibility with the standard Illumina Primers used. If you'd like a second opinion on the compatibility of your primers, we'd be more than happy to sit down with you and verify the primer design based on your constructs.		When submitting [[BioMicroCenter:Sequencing\|'''custom primers''']], be sure to verify their compatibility with the standard Illumina Primers used. If you'd like a second opinion on the compatibility of your primers, we'd be more than happy to sit down with you and verify the primer design based on your constructs.
		+
		+	Another important aspect to consider is the fact that clustering conditions differ when comparing the HiSeq to the MiSeq. The MiSeq clusters at about 5 degrees higher than the cBot, which is used to prepare flowcells for the HiSeq. This means that all custom primers must be designed appropriately so there Tm's are compatible with whatever sequencing route you choose.

	== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==		== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==

Scott J. Morin: /* Custom Primers */

2013-04-05T19:59:25Z

Custom Primers

←Older revision		Revision as of 19:59, 5 April 2013
Line 12:		Line 12:

	=== Custom Primers ===		=== Custom Primers ===
-	When submitting [[BioMicroCenter:Sequencing~~:Custom Primers~~\|'''custom primers''']], be sure to verify their compatibility with the standard Illumina Primers used. If you'd like a second opinion on the compatibility of your primers, we'd be more than happy to sit down with you and verify the primer design based on your constructs.	+	When submitting [[BioMicroCenter:Sequencing\|'''custom primers''']], be sure to verify their compatibility with the standard Illumina Primers used. If you'd like a second opinion on the compatibility of your primers, we'd be more than happy to sit down with you and verify the primer design based on your constructs.

	== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==		== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==

Scott J. Morin at 19:58, 5 April 2013

2013-04-05T19:58:21Z

←Older revision		Revision as of 19:58, 5 April 2013
Line 12:		Line 12:

	=== Custom Primers ===		=== Custom Primers ===
-	When submitting [[BioMicroCenter:Sequencing\|'''custom primers''']], be sure to verify their compatibility with the standard Illumina Primers used. If you'd like a second opinion on the compatibility of your primers, we'd be more than happy to sit down with you and verify the primer design based on your constructs.	+	When submitting [[BioMicroCenter:Sequencing:Custom Primers\|'''custom primers''']], be sure to verify their compatibility with the standard Illumina Primers used. If you'd like a second opinion on the compatibility of your primers, we'd be more than happy to sit down with you and verify the primer design based on your constructs.

	== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==		== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==

Scott J. Morin at 19:54, 5 April 2013

2013-04-05T19:54:37Z

←Older revision		Revision as of 19:54, 5 April 2013
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	== SUBMISSIONS ==		== SUBMISSIONS ==
	=== Volume/Concentration ===		=== Volume/Concentration ===
-	The volume and concentration needed for submission will depend on the type of sample prep. However, if you are submitting prepped, sequence-ready samples, we require a minimum of 10uL at a concentration of at least 1.0nM. This allows us to perform quality control and have enough of the library for clustering.	+	The volume and concentration needed for submission will depend on the type of sample prep. However, if you are submitting prepped, sequence-ready samples, we require a minimum of 10uL at a concentration of at least 1.0nM. This allows us to perform quality control and have enough of the library for clustering. Any samples less than 1.0nM cause significant difficulties with clustering the flowcell, which is why we cannot guarantee optimal read count and quality should you like us to proceed with sequencing a low concentration sample.
		+
		+	=== Custom Primers ===
		+	When submitting [[BioMicroCenter:Sequencing\|'''custom primers''']], be sure to verify their compatibility with the standard Illumina Primers used. If you'd like a second opinion on the compatibility of your primers, we'd be more than happy to sit down with you and verify the primer design based on your constructs.

	== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==		== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==

Scott J. Morin at 19:42, 5 April 2013

2013-04-05T19:42:17Z

←Older revision		Revision as of 19:42, 5 April 2013
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	'''PHONE:''' The main lab number is 617-715-4533 <BR>		'''PHONE:''' The main lab number is 617-715-4533 <BR>
	Our director, [[User:Stuart S. Levine\|Stuart Levine]], can be reached at 617-452-2949.		Our director, [[User:Stuart S. Levine\|Stuart Levine]], can be reached at 617-452-2949.
		+
		+	== SUBMISSIONS ==
		+	=== Volume/Concentration ===
		+	The volume and concentration needed for submission will depend on the type of sample prep. However, if you are submitting prepped, sequence-ready samples, we require a minimum of 10uL at a concentration of at least 1.0nM. This allows us to perform quality control and have enough of the library for clustering.

	== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==		== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==

Stuart S. Levine: /* HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED */

2012-08-29T02:07:31Z

HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED

←Older revision		Revision as of 02:07, 29 August 2012
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	== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==		== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==
-	This is a very hard question to answer because it involves a number of variables. The simplest answer is, samples preparation typically takes ~1 weeks for standard samples with all reagents on hand (QC, prep, QC). For newer or rarely used methods, the number can extend to a month if we need to gather reagents. Once the sample is ready, it goes in to the sequencing queue. This queue is often the longest part of the process. Once the full flowcell is ready and put on a sequencer, it takes ~1.3h per base to sequence (this used to be 1h but upgrades to the machines have slowed them down some). A 40nt read takes just over 2 days. Turn around (for PE samples) functionally takes about a 1/2 day. So a 100+100PE sample will take about 11 days once it is on the sequencer - if nothing goes wrong.	+	This is a very hard question to answer because it involves a number of variables. The simplest answer is, samples preparation typically takes ~1 weeks for standard samples with all reagents on hand (QC, prep, QC). For newer or rarely used methods, the number can extend to a month if we need to gather reagents. Once the sample is ready, it goes in to the sequencing queue. This queue is often the longest part of the process. Once the full flowcell is ready and put on a sequencer, it takes ~1.3h per base to sequence (this used to be 1h but upgrades to the machines have slowed them down some). A 40nt read takes just over 2 days. Turn around (for PE samples) functionally takes about a 1/2 day. So a 100+100PE sample will take about 11 days once it is on the sequencer - if nothing goes wrong. Overall, when the queue is flowing at full speed, a 40nt SE submission with sample preparation can be returned with data in right around 3 weeks. 40+40PE samples more typically take ~4-6 weeks and 80+80PE runs typically average ~6-8 weeks for [[BioMicroCenter:CoreDeps\|CORE lab members]] with the extra time coming from delays in filling out flowcells.

	GAII and MISEQ are much simpler. Once the sample is prepped and the machine is working, it will be loaded immediately. Total times should be less than 3 weeks.		GAII and MISEQ are much simpler. Once the sample is prepped and the machine is working, it will be loaded immediately. Total times should be less than 3 weeks.

Stuart S. Levine: /* Illumina Queue: Priority */

2012-08-29T02:02:23Z

Illumina Queue: Priority

←Older revision		Revision as of 02:02, 29 August 2012
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	\|-		\|-
	\| 3		\| 3
-	\| [BioMicroCenter:CoreDeps\|MIT CORE labs]	+	\| [[BioMicroCenter:CoreDeps\|MIT CORE labs]]
	\|-		\|-
	\| 4		\| 4

Stuart S. Levine: /* Illumina Queue: Priority */

2012-08-29T02:01:29Z

Illumina Queue: Priority

←Older revision		Revision as of 02:01, 29 August 2012
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	=== Illumina Queue: Priority ===		=== Illumina Queue: Priority ===
	{\|		{\|
-	\|	+	\|width=450\|
	The BioMicro Center queue operates on a tiered priority basis (see table). We hold to this priority schema as closely as we can while still needing to fill flowcells. Some caveats: Once a flowcell is quality controlled and "on deck" for clustering, that flowcell is considered locked and no new submissions will be added to it. Clustering can happen a week or more before loading. Once flowcells are clustered, their order is set barring the need for reruns.		The BioMicro Center queue operates on a tiered priority basis (see table). We hold to this priority schema as closely as we can while still needing to fill flowcells. Some caveats: Once a flowcell is quality controlled and "on deck" for clustering, that flowcell is considered locked and no new submissions will be added to it. Clustering can happen a week or more before loading. Once flowcells are clustered, their order is set barring the need for reruns.
	\|		\|
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	\|-		\|-
	\| 3		\| 3
-	\| MIT CORE labs	+	\| [BioMicroCenter:CoreDeps\|MIT CORE labs]
	\|-		\|-
	\| 4		\| 4
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	\|}		\|}
	\|}		\|}
-

	=== Failures ===		=== Failures ===

Stuart S. Levine: /* HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED */

2012-08-29T01:59:40Z

HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED

←Older revision		Revision as of 01:59, 29 August 2012
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	=== Illumina Queue: Priority ===		=== Illumina Queue: Priority ===
		+	{\|
		+	\|
		+	The BioMicro Center queue operates on a tiered priority basis (see table). We hold to this priority schema as closely as we can while still needing to fill flowcells. Some caveats: Once a flowcell is quality controlled and "on deck" for clustering, that flowcell is considered locked and no new submissions will be added to it. Clustering can happen a week or more before loading. Once flowcells are clustered, their order is set barring the need for reruns.
		+	\|
	{\| align="right", textalign="center", border=1		{\| align="right", textalign="center", border=1
	! Priority		! Priority
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	\| 5		\| 5
	\| non-MIT users		\| non-MIT users
		+	\|}
	\|}		\|}

-	The BioMicro Center queue operates on a tiered priority basis (see table). We hold to this priority schema as closely as we can while still needing to fill flowcells. Some caveats: Once a flowcell is quality controlled and "on deck" for clustering, that flowcell is considered locked and no new submissions will be added to it. Additionally, once a flowcell is clustered, all samples on that flowcell WILL BE BILLED, regardless of if the samples are withdrawn. Clustering can happen a week or more before loading. Once flowcells are clustered, their order is set barring the need for reruns.

	=== Failures ===		=== Failures ===