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== 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 20, 2013 ===


=== Aug 9, 2010 ===
We have noticed a number of technical issues with some Illumina runs. We want to share with you to make sure you are aware of some changes and newly identified technical issues with the platform and what we are doing to correct them where we can. All of these changes are from the Illumina side and none were especially well documented (some not at all). These issues are unlikely to be limited to the BMC, so samples from elsewhere on campus or around the country may also have these issues. Please read this as it may have some impact on your analyses. <BR><BR>
Dear Users,<br>
There have been a number of significant changes in the BioMicro Center in the past few months and there will be more to come. To keep you up to date, I will again be sending out a newsletter ever month or two with highlights of what is going on. Unlike previous newsletters, these will only be sent to those who have used the facility within the past year or so, so be sure to spread the word if you see items that might be of interest to others in your lab!
====New equipment====
A number of pieces of new equipment have been added to the BioMicro Center, particularly in the area of high throughput screening. First, through an equipment grant sponsored by Wendy Gilbert, we have added a second robotic fluidics machine that is specifically geared for screening 96 and 384 well plates.  Unlike the older robot, this Tecan has a plate manipulating arm that allows it to handle much larger experiments. We also have added the Fluidigm Biomark which has been relocated from E17 and we are also in the evaluation phase for the Nanostring nCounter. Both of these machines allow you to look at a large number of genes / SNPs across a large number of samples. The Biomark is a nanofluidic RT-PCR machine that creates large matrices (either 48x48 or 96x96) of samples and primers, allowing you to do close to 10,000 RT-PCR reactions on a plate. The nCounter uses a “code set” of up to 800 genes to hybridize to dozens or hundreds of samples, then visualizes the single molecule interactions. The nCounter is particularly interesting in that it does not require conversion of the sample to cDNA, or even purification of the RNA. Information about all of these instruments can be found on our website.
====New services====
We are happy to announce the beginning of sample preparation services for Illumina sequencing. We are introducing this service starting with double stranded DNA fragments (>100bp) such as de novo genomic sequencing, resequencing, ChIP-seq and RNA-seq that has been converted to cDNA. The service includes QC, end-repair, adaptor ligation, size selection and enrichment. Once samples are prepared, they are validated and added directly to the Illumina sequencing queue. Right now, this service is limited, but we are hoping to introduce multiplexing and RNA samples in the near future.
====Upcoming Events====
With so many changes both in new equipment and upgrades to current equipment we wanted to create an opportunity for you to learn more about the assays available in the facility. To help with this, we will be sponsoring a “Technology Seminar Series” this fall. The weekly seminars will be at noon on Mondays (lunch will be provided). Each week we will showcase a different technology in the facility and bring you up to date on the latest advances and future directions of the technology. We have asked the companies we have invited to bring their scientists to speak (not the sales team) so you have a chance to interact with them directly.
I hope you are having a great summer!<br>
-Stuart


Just to begin, all of these changes are subtle and not obvious in most cases directly from the sequencers. It was the rare cases that had dramatic effects that caused us to notice them. If you decide you need to have samples rerun, we will work with you to try to get Illumina to replace the reagents and to get the samples rerun. Unfortunately, there is no way we can possibly do bulk reruns of several months’ worth of studies.  <BR><BR>


=== May 13, 2010 ===
The most concerning issue is a dropout of GC rich regions in clustering. This has been an on-again off-again issue with Illumina that we have addressed over a year ago by improvements in amplification cycling conditions and enzyme selection. Some time, several months ago (we do not have a precise window), Illumina appears to have changed the chemistry of one of their clustering components and that caused a major change in performance on GC rich areas. This can be seen as an absence of reads from very GC rich areas but, because these areas are rare in most genomes, they cannot be seen on the flowcell wide metrics. This issue is found on current HiSeq and MiSeqV2 kits but not on MiSeqV1 kits nor, we suspect, on the GAII. We have been able to address this problem by adding a brief boiling step during NaOH denaturation of the samples and have implemented this as SOP starting about two weeks ago. This drop out of regions can cause significant issues for several studies – most notably ChIP analyses – when you are comparing data from different chemistries. <BR><BR>
In order to increase the space available for equipment in the BioMicro Center, we are doing a little more remodeling. Please note the following changes:
* The freezers have been relocated to the 304 hallway
* The RT-PCR machines will be moving to the 316 entry.
We hope this change will make accessing the [[BioMicroCenter:RTPCR|RT-PCR]] machines easier and will also create room for the [[BioMicroCenter:Tecan_Freedom_Evo|new Tecan EVO 150]], scheduled to arrive in early June. Keep an eye on this page for future updates!


=== April 19, 2010 ===
A second concern is one that has been reported in the community but we have not identified on our machines – yet – where samples from a run are being observed in the following run as minor contaminants. This issue is limited to the MiSeq and HiSeq2500 (we do not have the latter) where the tubes that add sample to the flowcell are not changed. This contamination is reported to be <1% and so would not show up on our quality metrics. However, if your MiSeq analyses are being based on finding a few reads in a large pool of discarded data or you are doing a number of sequential runs, you may wish to validate your data more carefully using an alternative technique such as qPCR or sanger sequencing. There is currently no technical fix to this problem.  <BR><BR>


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.
A third issue has been around for a while though we had not appreciated the implications. Illumina’s newer versions of basecalling software have become less capable of handling uniform sequence (all A’s for example). In earlier versions, only 5 basepairs of variability were needed and intensities could be determined by the control lane we run on all HiSeq flowcells. Now, it appears that nt 1-25 all must have representation of all 4 bases at all positions, even with a control lane. This has always been an issue on the MISeq and we have solved it by spiking in 30%PhiX in the lane (as opposed to our normal 0.1% spike in). Similar solutions can be used on the HiSeq. Given this change, we are re-evaluating whether there is value in using the 8th lane as a control. The latest version of MiSeq software (only a couple days old) supposedly allows us to lower the fraction to 5%, but how successful this is remains to be seen. Base rearrangement with the GAII allows the GAII to avoid this issue. <BR><BR>


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.  
Finally, it appears that custom priming on the MiSeq is not the same as custom priming on the HiSeq and GAII. It can still be done, but the Tm requirement is much higher. Primers that work on the HiSeq may fail on the MiSeq. As long as your Tm matches or exceeds the Tm used for Illumina primers, the MiSeq should work, but the MiSeq’s different chemistry (formamide instead of heat denaturation) is less forgiving. <BR><BR>


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 [[Media:Nanostring_abstract.pdf‎|ABSTRACT]] for the talk.
In summary, we have a number of technical challenges that may (or may not) effect you and we want to make sure you have all the information we can give you. I want to thank the researchers and labs that have been very patient as we have struggled running their samples which led us to identify these problems. If you believe these issues have effected your data, please do not hesitate to contact me and we can discuss how to move forward. <BR><BR>


=== 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!
=== MARCH 11, 2013 ===
Quick update from BioMicro: <BR><BR>
The [[BioMicroCenter:Wafergen|Wafergen qPCR system]] is now operational. We have done a couple pilot experiments so far and it does seem to work, if there are a few more limitations than we anticipated. We are working with Wafergen to see how many of these can be alleviated but you are more than welcome to try it out and see if it would be useful to you. They have given us quite competitive pricing that is a lot lower than the cost for the [[BioMicroCenter:Fluidigm|Fluidigm BioMark]] . Please email us if you are interested in training.


=== March 2010 ===
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"
! 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.


=== 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.


|-
|valign="top" width="45%"|


===RECENT & UPCOMING CHANGES===


{{BioMicroCenter:News/Changes/Content}}


|valign="top"|


<B><BIG>PREVIOUS NEWSLETTERS </BIG></B>
== 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 [http://biology.mit.edu Department of Biology], the [http://ki.mit.edu Koch Institute for Integrative Cancer Research], the [http://be.mit.edu Department of Biological Engineering] and the [http://cehs.mit.edu MIT 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 [http://ki.mit.edu Koch Institute] as the [http://ki.mit.edu/sbc/microarray MicroArray Technologies Core] and as part of the [http://ki.mit.edu/sbc/bioinformatics Bioinformatics and Computing Core] and the [http://cehs.mit.edu MIT Center for Environmental Health Sciences] as part of the [http://cehs.mit.edu/facilities.html#Genomics_and_Bioinformatics_Core Genomics and Imaging Core]<BR><BR>
|'''[[BioMicroCenter:News/2009|2009]]'''
 
|-
Experimental and analytical work done in the BioMicro Center is funded by the NIH and must be made available through the NIH's open access policy. All Koch Institute and CEHS labs '''must''' acknowledge their core grants for work done in the core with the following language.
|{{BioMicroCenter:News/2009/Content}}
* KI ''"This work was funded by the National Cancer Institute of the NIH under award P30-CA14051"''
|-
* CEHS ''"This work was funded by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109"''
|'''[[BioMicroCenter:News/2008|2008]]'''
 
|-
== PUBLICATIONS ==
|{{BioMicroCenter:News/2008/Content}}
'''2013'''<BR><BR>
|}
<biblio>
#Paper1 pmid=23662897 <!- BMC Paper->
#Paper2 pmid=23657361 <!- HD Chisholm->
#Paper3 pmid=23352431 <!- HD.VB Boyer->
#Paper4 pmid=23630078 <!- CW.AJ Sharp->
#Paper5 pmid=23523371 <!- CW Jacks->
</biblio>
'''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 ==


'''[[BioMicroCenter:News2012|2012]]'''<BR>
'''[[BioMicroCenter:News2011|2011]]'''<BR>
'''[[BioMicroCenter:News2010|2010]]'''
<br>
<br>
<B><BIG>RECENT CHANGES TO THE WEBSITE <\BIG><\B>
 
== RECENT CHANGES TO THE WEBSITE ==
{{BioMicroChanges}}
{{BioMicroChanges}}


|}
|}

Revision as of 08:12, 28 May 2013

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

.

Welcome to the MIT BIOMICRO CENTER

BioMicro Center News

APRIL 20, 2013

We have noticed a number of technical issues with some Illumina runs. We want to share with you to make sure you are aware of some changes and newly identified technical issues with the platform and what we are doing to correct them where we can. All of these changes are from the Illumina side and none were especially well documented (some not at all). These issues are unlikely to be limited to the BMC, so samples from elsewhere on campus or around the country may also have these issues. Please read this as it may have some impact on your analyses.

Just to begin, all of these changes are subtle and not obvious in most cases directly from the sequencers. It was the rare cases that had dramatic effects that caused us to notice them. If you decide you need to have samples rerun, we will work with you to try to get Illumina to replace the reagents and to get the samples rerun. Unfortunately, there is no way we can possibly do bulk reruns of several months’ worth of studies.

The most concerning issue is a dropout of GC rich regions in clustering. This has been an on-again off-again issue with Illumina that we have addressed over a year ago by improvements in amplification cycling conditions and enzyme selection. Some time, several months ago (we do not have a precise window), Illumina appears to have changed the chemistry of one of their clustering components and that caused a major change in performance on GC rich areas. This can be seen as an absence of reads from very GC rich areas but, because these areas are rare in most genomes, they cannot be seen on the flowcell wide metrics. This issue is found on current HiSeq and MiSeqV2 kits but not on MiSeqV1 kits nor, we suspect, on the GAII. We have been able to address this problem by adding a brief boiling step during NaOH denaturation of the samples and have implemented this as SOP starting about two weeks ago. This drop out of regions can cause significant issues for several studies – most notably ChIP analyses – when you are comparing data from different chemistries.

A second concern is one that has been reported in the community but we have not identified on our machines – yet – where samples from a run are being observed in the following run as minor contaminants. This issue is limited to the MiSeq and HiSeq2500 (we do not have the latter) where the tubes that add sample to the flowcell are not changed. This contamination is reported to be <1% and so would not show up on our quality metrics. However, if your MiSeq analyses are being based on finding a few reads in a large pool of discarded data or you are doing a number of sequential runs, you may wish to validate your data more carefully using an alternative technique such as qPCR or sanger sequencing. There is currently no technical fix to this problem.

A third issue has been around for a while though we had not appreciated the implications. Illumina’s newer versions of basecalling software have become less capable of handling uniform sequence (all A’s for example). In earlier versions, only 5 basepairs of variability were needed and intensities could be determined by the control lane we run on all HiSeq flowcells. Now, it appears that nt 1-25 all must have representation of all 4 bases at all positions, even with a control lane. This has always been an issue on the MISeq and we have solved it by spiking in 30%PhiX in the lane (as opposed to our normal 0.1% spike in). Similar solutions can be used on the HiSeq. Given this change, we are re-evaluating whether there is value in using the 8th lane as a control. The latest version of MiSeq software (only a couple days old) supposedly allows us to lower the fraction to 5%, but how successful this is remains to be seen. Base rearrangement with the GAII allows the GAII to avoid this issue.

Finally, it appears that custom priming on the MiSeq is not the same as custom priming on the HiSeq and GAII. It can still be done, but the Tm requirement is much higher. Primers that work on the HiSeq may fail on the MiSeq. As long as your Tm matches or exceeds the Tm used for Illumina primers, the MiSeq should work, but the MiSeq’s different chemistry (formamide instead of heat denaturation) is less forgiving.

In summary, we have a number of technical challenges that may (or may not) effect you and we want to make sure you have all the information we can give you. I want to thank the researchers and labs that have been very patient as we have struggled running their samples which led us to identify these problems. If you believe these issues have effected your data, please do not hesitate to contact me and we can discuss how to move forward.


MARCH 11, 2013

Quick update from BioMicro:

The Wafergen qPCR system is now operational. We have done a couple pilot experiments so far and it does seem to work, if there are a few more limitations than we anticipated. We are working with Wafergen to see how many of these can be alleviated but you are more than welcome to try it out and see if it would be useful to you. They have given us quite competitive pricing that is a lot lower than the cost for the Fluidigm BioMark . Please email us if you are interested in training.


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 for Integrative Cancer Research, the Department of Biological Engineering and the MIT 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 Institute 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

Experimental and analytical work done in the BioMicro Center is funded by the NIH and must be made available through the NIH's open access policy. All Koch Institute and CEHS labs must acknowledge their core grants for work done in the core with the following language.

  • KI "This work was funded by the National Cancer Institute of the NIH under award P30-CA14051"
  • CEHS "This work was funded by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109"

PUBLICATIONS

2013

  1. Gravina MT, Lin JH, and Levine SS. Lane-by-lane sequencing using Illumina's Genome Analyzer II. Biotechniques. 2013 May;54(5):265-9. DOI:10.2144/000114032 | PubMed ID:23662897 | HubMed [Paper1]
  2. Kelly L, Ding H, Huang KH, Osburne MS, and Chisholm SW. Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent. ISME J. 2013 Sep;7(9):1827-41. DOI:10.1038/ismej.2013.58 | PubMed ID:23657361 | HubMed [Paper2]
  3. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, and Boyer LA. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell. 2013 Jan 31;152(3):570-83. DOI:10.1016/j.cell.2013.01.003 | PubMed ID:23352431 | HubMed [Paper3]
  4. Gurtan AM, Ravi A, Rahl PB, Bosson AD, JnBaptiste CK, Bhutkar A, Whittaker CA, Young RA, and Sharp PA. Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts. Genes Dev. 2013 Apr 15;27(8):941-54. DOI:10.1101/gad.215376.113 | PubMed ID:23630078 | HubMed [Paper4]
  5. Snyder EL, Watanabe H, Magendantz M, Hoersch S, Chen TA, Wang DG, Crowley D, Whittaker CA, Meyerson M, Kimura S, and Jacks T. Nkx2-1 represses a latent gastric differentiation program in lung adenocarcinoma. Mol Cell. 2013 Apr 25;50(2):185-99. DOI:10.1016/j.molcel.2013.02.018 | PubMed ID:23523371 | HubMed [Paper5]
All Medline abstracts: PubMed | HubMed

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

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18 April 2024

     15:01  Pan:Who we are‎ diffhist +14‎ Taopan talk contribs
      15:00  Pan:Methods‎‎ 2 changes history +456‎ [Taopan‎ (2×)]
     
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     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)
     
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     12:12  BioMicroCenter:Tecan Freedom Evo‎‎ 7 changes history +1,746‎ [Noelani Kamelamela‎ (7×)]
     
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10:13 (cur | prev) +7‎ Noelani Kamelamela talk contribs (→‎verrity Chemagic 360)
     
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     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×)]
     
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     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×)]
     
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     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×)]
     
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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)
     
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     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×)]
     
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