BioMicroCenter:News: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
(33 intermediate revisions by 4 users not shown)
Line 1: Line 1:
{{BioMicroCenter}}
{{BioMicroCenter}}


.
== Welcome to the MIT BIOMICRO CENTER ==


{|
{|
|rowspan=2 valign=top style="width:55%;padding-right:10px;"|  
|valign=top style="width:60%;padding-right:10px;"|  
== BioMicro Center News ==


=== April 19, 2010 ===


Starting next month, the [http://mit.edu/ki/index.html Koch Institute] and the MIT BioMicro Center will be hosting a [http://www.nanostring.com/ Nanostring] nCounter system on a trial basis. The [http://www.nanostring.com/products/ncounter/ nCounter system] is a [http://www.nanostring.com/applications/technology/ single molecule visualizer] that quantitatively detects RNA and other nucleic acids using a hybridization system in a highly multiplex manner. The system uses color-coded molecular barcodes to digitally count nucleic acid molecules in solution. The system does not use enzymes for detecting the nucleic acids, allowing direct measurements of mRNA from a variety of input materials including degraded RNA or crude cell lysates.


The instruments will be located in the BioMicro Center and will be available to all members of the MIT community. We will be using this time to gauge the level of interest in the nCounter and whether it would be a viable system to purchase.  
=== JANUARY 9, 2013 ===
Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of. <BR><BR>
First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.  <BR><BR>
During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.  <BR><BR>
Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting  how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week.
If you have any concerns, please do not hesitate to contact me.


If you are interested in learning more, we will be hosting a seminar with [http://www.nanostring.com/ Nanostring] representatives on April 30th. The seminar will be at 11am in 68-181. Nanostring representatives will be available after the talk to discuss the instruments and specific applications. More information is in the ABSTRACT for the talk.




=== April 1, 2010 ===


Thanks to the generosity of a grant from the [http://www.moore.org/ Moore Foundation] to Dr. Penny Chisholm and ARRA funding to Dr. Chris Burge the BioMicro Center will be significantly expanding our sequencing capacity over the next 4-6 months. The first step of this expansion begins today with the addition of a new [http://www.illumina.com/systems/genome_analyzer_iix.ilmn GAIIx] and [http://www.illumina.com/systems/genome_analyzer/cbot.ilmn cBot] from Illumina. We are working hard to get ''"Ryland"'' and ''"Agustus Gloop"'' up and running and we hope to be able to shorten our queue times very soon!
|valign="top"|


=== March 2010 ===
== ABOUT THE BIOMICRO CENTER ==
Due to an increase in the cost of Illumina reagents, increase in data file size, and the complexity of sample preps, we have had to increase, slightly, the cost of Illumina sequencing. These new rates will be effective on samples submitted after April 1, 2010. Samples already in the queue will use the current rates.


{| border=1 align="right"
The MIT BioMicro Center was founded in 2000 as the core bio-fabrication and microarray processing facility at MIT. The Center is a joint endeavor between the [Department of Biology], the [Koch Institute], the [Department of Biological Engineering] and the [Center for Environmental Health Sciences.] The BioMicro Center offers a wide range of genomic services to researchers at MIT. The majority of services rendered pertain to massively parallel sequencing using the Illumina Genome Analyzer (both library preparation and sequencing). Commercial array processing and include both the Affymetrix Gene Chip and Agilent DNA array platforms continues to be a significant portion of our portfolio. Real-time PCR and Agilent BioAnalyzer services are available in the facility both as services available to researchers, as well as for quality control of microarray and sequencing samples. In addition, the Center has a presence in high-throughput screening with robotics and plate reading as well as informatics and computational support. The BioMicro Center serves the Koch Instistute as the MicroArray Technologies Core and as part of the Bioinformatics and Computing Core and the MIT Center for Environmental Health Sciences as part of the Genomics and Imaging Core<BR><BR>
! ILLUMINA SEQUENCING
!width=100| MIT - current
!width=100| MIT - April 1, 2010
!width=100| unit
! Notes
|-
| Single End (36nt)
|align="right"| $805
|align="right"| $860
|align="center"| per lane
| inlcudes quality control (RT-PCR or BioAnalyzer), sequencing, genome alignment and data storage of Firecrest files for 2 yrs.
|-
| Paired End (36+36nt)
|align="right"| $1,385
|align="right"| $1,450
|align="center"| per lane
|
|-
| Add'l 36nt
|align="right"| $295
|align="right"| $300
|align="center"| per lane
| 
|-
| Sample Multiplexing
|align="right"| $0
|align="right"| $50
|align="center"| per 10 samples combined
| Combined over the whole order. Only applies to samples combined by BCM technicians.
|-
| Repriming
|align="right"| $200
|align="right"| $300
|align="center"| per flow cell
| Uses 6nt. Cost is divided by number of lanes requiring repriming. Repriming is required for standard Illumina multiplexing.
|-
|}
<BR>
Non-MIT rates are 30% higher for academic institutions and 50% highers for non-academic institutions. Priority is given to samples from CORE facilities.


== PUBLICATIONS ==
'''2013'''<BR><BR>
'''2012'''<BR><BR>
<biblio>
#Paper1 pmid=22981692 <!-SL Boyer: Heart->
#Paper2 pmid=22847430 <!-SL Saeij->
#Paper3 pmid=22102570 <!-HD Chisholm->
</biblio>
'''2011'''<BR><BR>
<biblio>
#Paper1 pmid=21892155 <!-SL Sur->
</biblio>
'''2010'''<BR><BR>
<biblio>
#Paper1 pmid=20720539 <!-SL Young->
#Paper2 pmid=20581084 <!-SL Zwaka->
</biblio>
'''2009'''<BR><BR>
<biblio>
#Paper1 pmid=19531355 <!-SL Amon->
</biblio>


|-
== PREVIOUS NEWSLETTERS ==
|valign="top" width="45%"|
 
===RECENT & UPCOMING CHANGES===
 
{{BioMicroCenter:News/Changes/Content}}


'''[[BioMicroCenter:News2012|2012]]'''<BR>
'''[[BioMicroCenter:News2011|2011]]'''<BR>
'''[[BioMicroCenter:News2010|2010]]'''
<br>


<B><BIG>PREVIOUS NEWSLETTERS </BIG></B>
== RECENT CHANGES TO THE WEBSITE ==
 
{|
|'''[[BioMicroCenter:News/2009|2009]]'''
|-
|{{BioMicroCenter:News/2009/Content}}
|-
|'''[[BioMicroCenter:News/2008|2008]]'''
|-
|{{BioMicroCenter:News/2008/Content}}
|}
 
<br>
<B><BIG>RECENT CHANGES TO THE WEBSITE <\BIG><\B>
{{BioMicroChanges}}
{{BioMicroChanges}}


|}
|}

Revision as of 09:54, 30 January 2013

HOME -- SEQUENCING -- LIBRARY PREP -- HIGH-THROUGHPUT -- COMPUTING -- OTHER TECHNOLOGY

.

Welcome to the MIT BIOMICRO CENTER

BioMicro Center News

JANUARY 9, 2013

Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of.

First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.

During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.

Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week. If you have any concerns, please do not hesitate to contact me.



ABOUT THE BIOMICRO CENTER

The MIT BioMicro Center was founded in 2000 as the core bio-fabrication and microarray processing facility at MIT. The Center is a joint endeavor between the [Department of Biology], the [Koch Institute], the [Department of Biological Engineering] and the [Center for Environmental Health Sciences.] The BioMicro Center offers a wide range of genomic services to researchers at MIT. The majority of services rendered pertain to massively parallel sequencing using the Illumina Genome Analyzer (both library preparation and sequencing). Commercial array processing and include both the Affymetrix Gene Chip and Agilent DNA array platforms continues to be a significant portion of our portfolio. Real-time PCR and Agilent BioAnalyzer services are available in the facility both as services available to researchers, as well as for quality control of microarray and sequencing samples. In addition, the Center has a presence in high-throughput screening with robotics and plate reading as well as informatics and computational support. The BioMicro Center serves the Koch Instistute as the MicroArray Technologies Core and as part of the Bioinformatics and Computing Core and the MIT Center for Environmental Health Sciences as part of the Genomics and Imaging Core

PUBLICATIONS

2013

2012

  1. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, and Bruneau BG. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28;151(1):206-20. DOI:10.1016/j.cell.2012.07.035 | PubMed ID:22981692 | HubMed [Paper1]
  2. Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, and Saeij JP. Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity. Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13458-63. DOI:10.1073/pnas.1117047109 | PubMed ID:22847430 | HubMed [Paper2]
  3. Kelly L, Huang KH, Ding H, and Chisholm SW. ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage. Nucleic Acids Res. 2012 Jan;40(Database issue):D632-40. DOI:10.1093/nar/gkr1022 | PubMed ID:22102570 | HubMed [Paper3]
All Medline abstracts: PubMed | HubMed

2011

  1. Mellios N, Sugihara H, Castro J, Banerjee A, Le C, Kumar A, Crawford B, Strathmann J, Tropea D, Levine SS, Edbauer D, and Sur M. miR-132, an experience-dependent microRNA, is essential for visual cortex plasticity. Nat Neurosci. 2011 Sep 4;14(10):1240-2. DOI:10.1038/nn.2909 | PubMed ID:21892155 | HubMed [Paper1]

2010

  1. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, and Young RA. Mediator and cohesin connect gene expression and chromatin architecture. Nature. 2010 Sep 23;467(7314):430-5. DOI:10.1038/nature09380 | PubMed ID:20720539 | HubMed [Paper1]
  2. Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, and Zwaka TP. Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells. Genes Dev. 2010 Jul 15;24(14):1479-84. DOI:10.1101/gad.1935210 | PubMed ID:20581084 | HubMed [Paper2]
All Medline abstracts: PubMed | HubMed

2009

  1. Boselli M, Rock J, Unal E, Levine SS, and Amon A. Effects of age on meiosis in budding yeast. Dev Cell. 2009 Jun;16(6):844-55. DOI:10.1016/j.devcel.2009.05.013 | PubMed ID:19531355 | HubMed [Paper1]

PREVIOUS NEWSLETTERS

2012
2011
2010

RECENT CHANGES TO THE WEBSITE

List of abbreviations:
N
This edit created a new page (also see list of new pages)
m
This is a minor edit
b
This edit was performed by a bot
(±123)
The page size changed by this number of bytes

18 April 2024

     15:01  Pan:Who we are‎ diffhist +14‎ Taopan talk contribs
      15:00  Pan:Methods‎‎ 2 changes history +456‎ [Taopan‎ (2×)]
     
15:00 (cur | prev) +2‎ Taopan talk contribs
     
14:59 (cur | prev) +454‎ Taopan talk contribs
     14:56  Pan:Publications‎‎ 2 changes history +396‎ [Taopan‎ (2×)]
     
14:56 (cur | prev) +74‎ Taopan talk contribs
     
14:54 (cur | prev) +322‎ Taopan talk contribs
     13:03  BioMicroCenter:Pricing‎ diffhist +166‎ Challee talk contribs
      12:58  BioMicroCenter:Singular Sequencing‎‎ 2 changes history +124‎ [Challee‎ (2×)]
     
12:58 (cur | prev) +14‎ Challee talk contribs (→‎Things to Consider)
     
12:57 (cur | prev) +110‎ Challee talk contribs
     12:12  BioMicroCenter:Tecan Freedom Evo‎‎ 7 changes history +1,746‎ [Noelani Kamelamela‎ (7×)]
     
12:12 (cur | prev) +4‎ Noelani Kamelamela talk contribs
     
12:12 (cur | prev) +3‎ Noelani Kamelamela talk contribs
     
10:13 (cur | prev) +7‎ Noelani Kamelamela talk contribs (→‎verrity Chemagic 360)
     
10:08 (cur | prev) −42‎ Noelani Kamelamela talk contribs (→‎verrity Chemagic 360)
     
10:08 (cur | prev) +86‎ Noelani Kamelamela talk contribs (→‎verrity Chemagic 360)
     
09:34 (cur | prev) +23‎ Noelani Kamelamela talk contribs (→‎verrity Chemagic 360)
     
09:32 (cur | prev) +1,665‎ Noelani Kamelamela talk contribs
     11:42  3D Cell Culture - McLean Taggart, Emma Villares, Maximillian Marek, Scott LeBlanc, Adam Lyons and Jacob Belden‎ diffhist −3‎ Sarah L. Perry talk contribs
      09:35  BioMicroCenter‎‎ 2 changes history +92‎ [Noelani Kamelamela‎ (2×)]
     
09:35 (cur | prev) +60‎ Noelani Kamelamela talk contribs
     
09:20 (cur | prev) +32‎ Noelani Kamelamela talk contribs
     09:32 Upload log Noelani Kamelamela talk contribs uploaded File:Chemagic360.jpg ‎(from manual)

17 April 2024

      15:34  BioMicroCenter:Element Sequencing‎‎ 3 changes history +295‎ [Challee‎ (3×)]
     
15:34 (cur | prev) +195‎ Challee talk contribs
     
14:22 (cur | prev) +100‎ Challee talk contribs
     
14:07 (cur | prev) 0‎ Challee talk contribs
     13:10  BioMicroCenter:SingleCell‎ diffhist +30‎ Noelani Kamelamela talk contribs (→‎10X CHROMIUM X)
     12:43  BioMicroCenter‎ diffhist −15‎ Noelani Kamelamela talk contribs

16 April 2024

 N    19:59  Nanoimprint Lithography (NIL) - Carter Paul‎‎ 10 changes history +7,205‎ [CarterPaul‎ (10×)]
     
19:59 (cur | prev) +769‎ CarterPaul talk contribs (→‎Thermal NIL Process)
     
19:53 (cur | prev) 0‎ CarterPaul talk contribs (→‎Thermal NIL Process)
     
19:53 (cur | prev) 0‎ CarterPaul talk contribs (→‎Thermal NIL Process)
     
19:52 (cur | prev) +1‎ CarterPaul talk contribs (→‎Thermal NIL Process)
     
19:50 (cur | prev) +202‎ CarterPaul talk contribs (→‎Thermal NIL Process)
     
19:17 (cur | prev) −20‎ CarterPaul talk contribs (→‎References)
     
19:17 (cur | prev) −1‎ CarterPaul talk contribs
     
19:11 (cur | prev) +4,278‎ CarterPaul talk contribs
     
18:53 (cur | prev) +1,891‎ CarterPaul talk contribs
N    
18:42 (cur | prev) +85‎ CarterPaul talk contribs (Created page with "{{Template:CHEM-ENG590E}} =Motivation= =Introduction to NIL= =Thermal NIL Process=")
     19:40 Upload log CarterPaul talk contribs uploaded File:NIL1.png ‎
N    18:40  3D Cell Culture - McLean Taggart, Emma Villares, Maximillian Marek, Scott LeBlanc, Adam Lyons and Jacob Belden‎ diffhist +24,060‎ CarterPaul talk contribs (Created page with "{{Template:CHEM-ENG590E}} ==Introduction== While most microfluidic devices incorporate a 2D cell culture design, in which a single layer of cells is grown on the bottom of a device, these systems suffer from poor <i>in vivo</i> mimicry, as, in the human body, most cells grow in all directions.<sup>https://doi.org/10.5114/aoms.2016.63743 1</sup> To address this limitation, 3D cell culture devices have been developed - in w...")
      18:38  CHEM-ENG590E:Wiki Textbook‎‎ 2 changes history +63‎ [CarterPaul‎ (2×)]
     
18:38 (cur | prev) +50‎ CarterPaul talk contribs (→‎Chapter 1 - Microfabrication)
     
18:37 (cur | prev) +13‎ CarterPaul talk contribs
     18:36  3D Cell Culture - McLean Taggart, Emma Villares, Maximillian Marek, Scott LeBlanc, and Adam Lyons‎ diffhist +5,343‎ CarterPaul talk contribs (Added a Technique and applications section)
      10:20  Yarn Microfluidics - Roger Dirth‎‎ 11 changes history +406‎ [Rcostello‎ (11×)]
     
10:20 (cur | prev) +41‎ Rcostello talk contribs (→‎Applications)
     
10:19 (cur | prev) +36‎ Rcostello talk contribs (→‎Applications)
     
10:18 (cur | prev) +36‎ Rcostello talk contribs (→‎Introduction)
     
10:17 (cur | prev) +38‎ Rcostello talk contribs (→‎Fabrication)
     
10:17 (cur | prev) +38‎ Rcostello talk contribs (→‎Washburn Equation)
     
10:16 (cur | prev) +38‎ Rcostello talk contribs (→‎Wicking Rate)
     
10:16 (cur | prev) +37‎ Rcostello talk contribs (→‎Introduction)
     
10:15 (cur | prev) +36‎ Rcostello talk contribs (→‎Wicking Rate)
     
10:14 (cur | prev) +36‎ Rcostello talk contribs (→‎Fabrication)
     
10:14 (cur | prev) +34‎ Rcostello talk contribs (→‎Applications)
     
10:14 (cur | prev) +36‎ Rcostello talk contribs (→‎Introduction)
Retrieved from "https://openwetware.org/mediawiki/index.php?title=BioMicroCenter:News&oldid=671628"