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Forum: RNA Sequencing 07-19-2012, 04:11 PM
Replies: 2
Views: 1,844
Posted By gendxdoc
Best RNA-Seq Analytical Pipeline to use - opinions ?

I am starting a project to examine differences in gene expression, across multiple regions of the brain -- from individuals with and without (controls) a neurodegenerative disorder.

My plan was to...
Forum: RNA Sequencing 05-25-2012, 02:56 PM
Replies: 11
Views: 7,399
Posted By gendxdoc
Low input micro RNA libraries

I would like to generate small RNA/miRNA libraries from small quantities of total RNA. The Illumina TruSeq Small RNA Library Prep kit requires an input of 1ug of total RNA for input.

Has...
Forum: Bioinformatics 01-04-2012, 10:38 PM
Replies: 16
Views: 4,010
Posted By gendxdoc
Long Term Data Storage

I am in the process of setting up a NGS core facility. I will be starting with a single HiSeq 1000 with an IlluminaCompute Tier0 analysis server. In a past life, I ran a NGS facility, in which we...
Forum: SOLiD 08-09-2011, 10:16 AM
Replies: 2
Views: 3,676
Posted By gendxdoc
Sorry --- didn't supply you with enough...

Sorry --- didn't supply you with enough information.

What I'm doing is using a single cell (or few cell) protocol for generating cDNA from total RNA -- been doing this for quite a while, works...
Forum: SOLiD 08-08-2011, 05:06 PM
Replies: 2
Views: 3,676
Posted By gendxdoc
SOLiD v3/v4 vs. 5500

Has anyone compared RNA-seq data generated on a SOLiD v3/v4 with a 5500 -- for the same sample ?

We've recently taken the same total RNA sample, constructed a 5500 library and performed a 50bp run...
Forum: General 08-01-2011, 07:58 PM
Replies: 7
Views: 3,092
Posted By gendxdoc
Confirmation sequencing technology

In a few months I will be setting up my 3rd NGS sequencing facility -- this time starting from scratch. I have a HiSeq system on the way, but need to select a technology for performing confirmation...
Forum: Sample Prep / Library Generation 09-24-2010, 04:38 PM
Replies: 1
Views: 4,512
Posted By gendxdoc
Target enrichment and CNV analysis

Is it possible to derive exon-size deletion/duplication information from target-enriched (array or in-solution), paired-end sequencing data ?

I'm working with a set of genes that frequently...
Forum: 454 Pyrosequencing 05-03-2010, 04:41 PM
Replies: 0
Views: 4,632
Posted By gendxdoc
454 Roche Titanium Run Costs

Hello All,

We are planning to purchase one of three (AB, Illumina or 454) next gen sequencing platforms and are comparing run costs.

Does anyone have a feel for the true run cost of the 454...
Forum: Bioinformatics 04-23-2010, 04:30 PM
Replies: 1
Views: 2,535
Posted By gendxdoc
Clinical Sequencing Software

Hello All,
Is anyone aware of a group or company developing a next gen sequencing pipeline (AB SOLiD, Illumina GA or Roche 454 platforms) for clinical diagnostics laboratories ?

We're really...
Forum: Bioinformatics 11-20-2009, 03:35 PM
Replies: 2
Views: 2,841
Posted By gendxdoc
ABI SOLiD Bioinformatic Services

Does anyone know of a fee for service facility that performs analytical services for ABI SOLiD data ? My colleagues and I have generated and are generating data for several projects and are looking...
Forum: Sample Prep / Library Generation 10-15-2009, 03:52 PM
Replies: 8
Views: 16,388
Posted By gendxdoc
Elaine -- This is a good result ! We're getting...

Elaine -- This is a good result ! We're getting ready to hybridize a pool of 16 indexed libraries with a SureSelect assay targeted at ~1.5Mb. We'll let you know how it goes.
Michael
Forum: Sample Prep / Library Generation 10-06-2009, 11:31 PM
Replies: 8
Views: 16,388
Posted By gendxdoc
Target enrichment from pooled libraries

Does anyone have any experience performing target enrichment from pooled libraries ? We're very interested in performing SureSelect (Agilent) in-solution capture (or array-based capture) with pooled...
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