Difference between revisions of "Template:SeqSubmissionGuide"

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=SEQUENCING SUBMISSION GUIDELINES=
 
=SEQUENCING SUBMISSION GUIDELINES=
  
You can download detailed guidelines in word format from [[Sample_Submission_Guide.pdf‎| here]].
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==STEP 1: REGISTRATION (FOR NEW CUSTOMERS ONLY)==
  
==STEP 1: REGISTRATION (FOR NEW CUSTOMERS ONLY)==
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* INTERNAL CUSTOMERS: Do NOT require to register in the system
  
* INTERNAL CUSTOMERS: Please [http://iona.wi.mit.edu/microarray/login/register.php| click here] to register in our system.
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* EXTERNAL CUSTOMERS: Have your lab administrator register in the Whitehead Cores Database - https://cores.wi.mit.edu/.
  
* EXTERNAL CUSTOMERS: Fill out a new customer form ([http://jura.wi.mit.edu/genomecorewiki/index.php/Forms| Available Here]) with billing information. Once the form is emailed you us, we will register you in our database and notify you when you can submit samples to us.
 
 
All external customers please obtain a purchase order number prior to your submission. If you need a quote, please email us at wibr-genome@wi.mit.edu or call us at 617-258-8803. Blanket purchase orders are preferred, if you plan to submit multiple projects over time.
 
All external customers please obtain a purchase order number prior to your submission. If you need a quote, please email us at wibr-genome@wi.mit.edu or call us at 617-258-8803. Blanket purchase orders are preferred, if you plan to submit multiple projects over time.
  
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===SUBMISSION OF SAMPLES FOR LIBRARY PREPARATION===
 
===SUBMISSION OF SAMPLES FOR LIBRARY PREPARATION===
  
Samples should be in a buffer that does not contain trace amounts of phenol or EDTA.  We will save and return any unused input material after libraries are successfully prepared. We will archive unused library.
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Samples should be in a buffer that does not contain trace amounts of phenol or EDTA.  We will save and return any unused input material after libraries are successfully prepared.
  
 
Below are our input requirements for Library Prep Service
 
Below are our input requirements for Library Prep Service
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| 200 to 400
 
| 200 to 400
 
| 500 to 1000
 
| 500 to 1000
| <50
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| 10-50
 
|-
 
|-
 
! scope="row"| ChIP
 
! scope="row"| ChIP
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| Variable (specify)
 
| Variable (specify)
 
| 10 to 50
 
| 10 to 50
| <50
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| 10-40
 
|-
 
|-
 
! scope="row"| RNA (total)
 
! scope="row"| RNA (total)
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| NA
 
| NA
 
| 100 to 1000
 
| 100 to 1000
| <50
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| 10-50
 
|}
 
|}
  
 
<nowiki>*</nowiki>Unless special arrangements are made with us in advance, we will assume that your genomic DNA sample has been fragmented, by sonication or otherwise, prior to submission.  
 
<nowiki>*</nowiki>Unless special arrangements are made with us in advance, we will assume that your genomic DNA sample has been fragmented, by sonication or otherwise, prior to submission.  
  
<nowiki>**</nowiki>We can work with less if necessary, but it is best if you elute your DNA in 50 ul or less if you believe we may need to use all of it.
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<nowiki>**</nowiki>We can work with less if necessary, but it is best if you elute your DNA in 50 ul or less if you believe we may need to use all of it. Please give us at least 10uL of sample to ensure we have enough for QC and prep.
 
 
  
 
===SUBMISSION OF PRE-PREPARED LIBRARIES===
 
===SUBMISSION OF PRE-PREPARED LIBRARIES===
We typically need 10-20 ul of each library at 5 ng/ul or greater. If your library is less concentrated than 5 ng/ul, we’ll quantify it to make sure we have enough to sequence. We will archive your leftover library.  
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We typically need 10-20 ul of each library at 5 ng/ul or greater. If your library is less concentrated than 5 ng/ul, we’ll quantify it to make sure we have enough to sequence.
  
  
  
 
==STEP 3: ONLINE SUBMISSION OF SEQUENCING LIBRARIES==
 
==STEP 3: ONLINE SUBMISSION OF SEQUENCING LIBRARIES==
*Please complete the online submission form (Available Here). Questions or problems related to the submission database should be directed to Sumeet Gupta at sgupta@wi.mit.edu
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*Please complete the online submission form ([http://jura.wi.mit.edu/genomecorewiki/index.php/Forms Link To Form Available Here]). Questions or problems related to the submission should be directed to Sumeet Gupta at sgupta@wi.mit.edu
  
 
*Every physical sample tube should have its own Genome Tech Core ID (GTC ID) number (automatically generated and emailed to you immediately after submission of the online form), even if you plan to multiplex them.  
 
*Every physical sample tube should have its own Genome Tech Core ID (GTC ID) number (automatically generated and emailed to you immediately after submission of the online form), even if you plan to multiplex them.  
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Whitehead Institute Genome Technology Core <br>
 
Whitehead Institute Genome Technology Core <br>
9 Cambridge Center, Room 325<br>
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455 Main Street, Room 325<br>
 
Cambridge, MA 02142
 
Cambridge, MA 02142
  
 
Please do not ship without first contacting someone in the lab, to make sure that we are here to receive your package. Do not rely on voicemail. Please wait until you hear back from someone.
 
Please do not ship without first contacting someone in the lab, to make sure that we are here to receive your package. Do not rely on voicemail. Please wait until you hear back from someone.

Latest revision as of 12:20, 30 September 2019

SEQUENCING SUBMISSION GUIDELINES

STEP 1: REGISTRATION (FOR NEW CUSTOMERS ONLY)

  • INTERNAL CUSTOMERS: Do NOT require to register in the system

All external customers please obtain a purchase order number prior to your submission. If you need a quote, please email us at wibr-genome@wi.mit.edu or call us at 617-258-8803. Blanket purchase orders are preferred, if you plan to submit multiple projects over time.


STEP 2: PREPARATION OF SAMPLES

SUBMISSION OF SAMPLES FOR LIBRARY PREPARATION

Samples should be in a buffer that does not contain trace amounts of phenol or EDTA. We will save and return any unused input material after libraries are successfully prepared.

Below are our input requirements for Library Prep Service

Sample Type Sonication/Fragmentation* Fragment Size (bp) Input requirements (ng)** Volume (ul)
Genomic Required 200 to 400 500 to 1000 10-50
ChIP Required Variable (specify) 10 to 50 10-40
RNA (total) NA NA 100 to 1000 10-50

*Unless special arrangements are made with us in advance, we will assume that your genomic DNA sample has been fragmented, by sonication or otherwise, prior to submission.

**We can work with less if necessary, but it is best if you elute your DNA in 50 ul or less if you believe we may need to use all of it. Please give us at least 10uL of sample to ensure we have enough for QC and prep.

SUBMISSION OF PRE-PREPARED LIBRARIES

We typically need 10-20 ul of each library at 5 ng/ul or greater. If your library is less concentrated than 5 ng/ul, we’ll quantify it to make sure we have enough to sequence.


STEP 3: ONLINE SUBMISSION OF SEQUENCING LIBRARIES

  • Please complete the online submission form (Link To Form Available Here). Questions or problems related to the submission should be directed to Sumeet Gupta at sgupta@wi.mit.edu
  • Every physical sample tube should have its own Genome Tech Core ID (GTC ID) number (automatically generated and emailed to you immediately after submission of the online form), even if you plan to multiplex them.
  • Please write your name GTC ID numbers on the tubes. We prefer 1.5 ml tubes.


STEP 4: DROP-OFF OR SHIPPING

When you are ready, you may hand deliver or ship samples them on dry ice to:

Whitehead Institute Genome Technology Core
455 Main Street, Room 325
Cambridge, MA 02142

Please do not ship without first contacting someone in the lab, to make sure that we are here to receive your package. Do not rely on voicemail. Please wait until you hear back from someone.