Forum: Epigenetics
06-23-2011, 09:53 AM
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Replies: 4
Views: 2,878
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Forum: Sample Prep / Library Generation
05-13-2011, 01:11 PM
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Replies: 13
Views: 5,901
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Forum: Illumina/Solexa
05-09-2011, 06:54 AM
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Replies: 7
Views: 4,493
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Forum: Core Facilities
05-05-2011, 09:37 AM
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Replies: 9
Views: 7,714
Any Experience with Otogenetics
We are sending a genomic DNA sample to Otogenetics for human exome sequencing. They will make the library, sequence and do some bioinformatics at a very reasonable intro price. They are also giving...
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Forum: Sample Prep / Library Generation
05-05-2011, 09:03 AM
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Replies: 2
Views: 2,235
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Forum: Illumina/Solexa
05-05-2011, 09:01 AM
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Replies: 7
Views: 4,493
Are you using the Egel specific ladders from...
Are you using the Egel specific ladders from Invitrogen? I use the 50 bp Egel ladder for my size selection of ChIP products and the isolated fragments correlate well with what we see on the...
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Forum: Illumina/Solexa
04-21-2011, 09:51 AM
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Replies: 76
Views: 44,252
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Forum: Illumina/Solexa
04-20-2011, 12:17 PM
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Replies: 76
Views: 44,252
I also use the E-gel 2% size select gels...
I also use the E-gel 2% size select gels following amplification. This gets rid of all the adaptor species in the libraries. I typically have plenty of library for sequencing.
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Forum: Epigenetics
10-22-2010, 08:42 AM
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Replies: 5
Views: 4,183
I don't have any experience with small cell...
I don't have any experience with small cell numbers. Are you pulling down a histone modification or a TF? The only publications I have seen using low cell numbers (10,000 cells) and successful...
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Forum: Epigenetics
09-01-2010, 12:14 PM
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Replies: 13
Views: 7,524
Thanks GKM,
I did not analyze the data...
Thanks GKM,
I did not analyze the data myself so I will have to ask our informatics person these questions. He is using CisGenome since he is the one who wrote the program. Do you think I should...
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Forum: Epigenetics
09-01-2010, 12:04 PM
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Replies: 13
Views: 7,524
Just wanted to add that this particular Myc...
Just wanted to add that this particular Myc antibody has been used by multiple labs for a number of years. There is a boat load of ChIP-chip and ChIP-seq data out there for Myc using this antibody...
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Forum: Epigenetics
09-01-2010, 12:01 PM
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Replies: 13
Views: 7,524
The libraries are made from ChIP products...
The libraries are made from ChIP products generated from a human cell line. Myc, the TF we study is known to bind to thousands of promoters and maybe 4000-5000 intergenic sites. My chromatin was...
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Forum: Epigenetics
09-01-2010, 10:57 AM
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Replies: 13
Views: 7,524
Hi GKM,
After ChIP but before library...
Hi GKM,
After ChIP but before library construction, I do qPCR and calculate a %TI for my TF antibody and for an IgG control. For a number of target promoters I see anywhere from 10 to 100's of...
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Forum: Epigenetics
09-01-2010, 09:17 AM
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Replies: 13
Views: 7,524
I have just encountered the same problem. Been...
I have just encountered the same problem. Been doing ChIP for years with the same antibody for a TF and it usually works beautifully. After making the libary, I validated 3-4 promoters that I know...
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Forum: Sample Prep / Library Generation
07-29-2010, 10:26 AM
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Replies: 1
Views: 1,811
Adaptors for ChIP-seq libraries
I have made a couple of ChIP-seq libraries using Illumina's DNA library kit. I diluted the adaptors 1:30 to compensate for much lower DNA input (10-20ng). I will be getting my sequencing data back...
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Forum: Introductions
07-28-2010, 07:33 AM
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Replies: 0
Views: 903
Hi from Baltimore
I'm now to Seq Answers but have already gotten a ton of info. Thanks for the site. I've been doing ChIP for many years but am just now venturing into the ChIP-seq world. I'm do to get my first...
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Forum: Sample Prep / Library Generation
07-28-2010, 07:18 AM
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Replies: 6
Views: 5,147
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Forum: Sample Prep / Library Generation
07-28-2010, 07:10 AM
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Replies: 2
Views: 3,802
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Forum: Sample Prep / Library Generation
07-13-2010, 10:42 AM
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Replies: 13
Views: 7,857
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Forum: Sample Prep / Library Generation
07-13-2010, 10:33 AM
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Replies: 0
Views: 1,847
New to ChIP-seq
Hi everyone:
I posted this same thing on another forum but thought it most useful here (sorry for the double post)
I've been lurking here for awhile and have finally decided to post. I have...
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Forum: Illumina/Solexa
07-13-2010, 10:29 AM
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Replies: 0
Views: 1,250
New to ChIP-seq
Hi everyone:
I've been lurking here for awhile and have finally decided to post. I have read many of the threads on generation of ChIP-seq libraries and have gained considerable knowledge about...
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