ChIP on Chip - Revision history

Volkert: /* Sample Submission Guidelines */

2010-06-22T20:59:46Z

‎Sample Submission Guidelines

Volkert at 04:13, 31 January 2009

2009-01-31T04:13:22Z

10.9.31.73 at 14:53, 6 October 2008

2008-10-06T14:53:35Z

Sgupta at 15:34, 15 September 2008

2008-09-15T15:34:50Z

Sgupta at 20:27, 17 March 2008

2008-03-17T20:27:28Z

Sgupta at 22:09, 13 March 2008

2008-03-13T22:09:16Z

New page

{{TopRightSideBar|
|title=ChIP-Seq
|image=expression.gif
|subtitle=ChIP-Seq
|highlights=

}}

We offer a ChIP-CHIP Service utilizing the 3 Plaforms.

Key highlights of the service:

Please see below for further details about the service.

== Sample Submission Guidelines ==

* Customer should submit atleast 5 ug of Total RNA or 2 ug of Samples enriched for miRNA.
* RNA concentration and quality should be quantified.
* Sample submission forms should be submitted along or before the samples are submitted. The form is available here.

== mRNA Detection Platform ==

* Affymetrix.
* Agilent

blah

== Hyb Quality Control ==

== Data Extraction ==

* Microarray images are scanned for a balanced view and saved in TIFF formats.
* Numerical intensities are extracted for each probes
* The results are organized which includes TIFF image files and intensity data files, which is made available to the customer in a CD.

== Analysis ==

== Pricing ==

@@ Line 15: / Line 15: @@
 == Sample Submission Guidelines ==
-Customers are urged to provide material which has been amplified by either by LM-PCR or by Sigma’s “GenomePlex-Whole Genome Amplification” protocol in their own laboratories. We are happy to work with you to suit your individual needs.
+Customers are urged to provide material which has been amplified by either by LM-PCR or by Sigma’s “GenomePlex-Whole Genome Amplification” protocol in their own laboratories. We will do the Bio-prime labeling before hybridizing to the arrays.
 == Platform ==

@@ Line 21: / Line 21: @@
 == Platform ==
-The Whitehead Institute Center for Microarray Technology primarily uses the Agilent ChIP-Chip platform. A complete description of Agilent’s ChIP-Chip platform, including arrays, reagents and protocols, can be found here:
+The Whitehead Institute Genome Technology Core primarily uses the Agilent ChIP-Chip platform. A complete description of Agilent’s ChIP-Chip platform, including arrays, reagents and protocols, can be found here:
 http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494
-The WICMT can also process samples on the Nimblegen and Affymetrix platforms.
+The WIGTC can also process samples on the Nimblegen and Affymetrix platforms.
 Most arrays can be ordered for customers by us. Some minimum orders may apply. Please make sure you specify which array types you would like on your sample submission form.

@@ Line 32: / Line 32: @@
 == Protocols ==
-The following link contains detailed protocols for all steps in ChIP-chip sample preparation.
+The following link contains detailed protocols for all steps in ChIP-chip sample preparation. [http://www.nature.com/nprot/journal/v1/n2/full/nprot.2006.98.html Nature protocols paper]
 An alternative protocol for amplification of immunoprecipitated DNA is the Sigma GenomePlex -Whole Genome Amplification kit. Details can be found here:

@@ Line 1: / Line 1: @@
 {{TopRightSideBar|
-|title=ChIP-Seq
+|title=ChIP-CHIP
 |image=expression.gif
-|subtitle=ChIP-Seq
+|subtitle=ChIP-CHIP
 |highlights=

@@ Line 7: / Line 7: @@
 }}
-We offer a ChIP-CHIP Service utilizing the 3 Plaforms.
+ChIP-Chip (Chromatin IP on Chip, also called Genome Wide Location Analysis) is a method for studying the regulation of gene expression on a genome-wide scale. Using microarrays that tile either the entire genome, or specific regions of interest like promoters, at high resolution, the interaction of transcriptional regulators and their genes of interest can be studied in detail. This powerful technique can be used to map cell growth, cell cycle, nutrient utilization, stress responses and development. Such insight can be crucial to developing therapeutics to treat disease.
-Key highlights of the service:
+ChIP-Chip service includes Invitrogen Bioprime labeling of amplified genomic DNA, hybridization, washing and scanning of arrays, as well as data extraction.
 Please see below for further details about the service.
@@ Line 15: / Line 15: @@
 == Sample Submission Guidelines ==
-* Customer should submit atleast 5 ug of Total RNA or 2 ug of Samples enriched for miRNA.
+Customers are urged to provide material which has been amplified by either by LM-PCR or by Sigma’s “GenomePlex-Whole Genome Amplification” protocol in their own laboratories. We are happy to work with you to suit your individual needs.
-== mRNA Detection Platform ==
+If you are ready to submit samples to the Whitehead Institute Center for Microarray Technology, please see our “forms” link, and submit the completed GWLA form to Jennifer Love at jlove@wi.mit.edu. External users, please have your PO number ready before you submit samples. Please don’t hesitate to call us with questions, to request an estimate, etc.
-* Affymetrix.
+== Platform ==
-blah
+The Whitehead Institute Center for Microarray Technology primarily uses the Agilent ChIP-Chip platform. A complete description of Agilent’s ChIP-Chip platform, including arrays, reagents and protocols, can be found here:
-== Hyb Quality Control ==
+An alternative protocol for amplification of immunoprecipitated DNA is the Sigma GenomePlex -Whole Genome Amplification kit. Details can be found here:
-== Data Extraction ==
+== Analysis ==
 * Microarray images are scanned for a balanced view and saved in TIFF formats.
@@ Line 34: / Line 45: @@
 * The results are organized which includes TIFF image files and intensity data files, which is made available to the customer in a CD.
-== Analysis ==
+Data in spreadsheet form, along with raw images, will be packaged and delivered either on DVD and/or by FTP. For further information on analysis please contact Sumeet Gupta.
-−
 == Pricing ==