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Forum: Sample Prep / Library Generation 05-10-2011, 02:22 PM
Replies: 1
Views: 1,777
Posted By sanush
smallRNA seq input amount question

Hi,
We have done many RNA seq experiments, but this will be our small RNA seq experiment. We are following small RNA library preparation using Total RNA sequencing kit. The protocol suggests...
Forum: RNA Sequencing 06-28-2010, 11:44 AM
Replies: 4
Views: 3,501
Posted By sanush
Thanks The ribo depletion was done using...

Thanks

The ribo depletion was done using ribominus eukaryotic kit..any suggestion for alternate kit
Forum: RNA Sequencing 06-28-2010, 10:34 AM
Replies: 4
Views: 3,501
Posted By sanush
Ribosomal removal problem

Hi all
We have been using ABI's Ribominus kit for the ribosomal removal for RNA seq experiment. After ribominus treatment we check it on the bioanalyzer and usually the ribosomal...
Forum: Bioinformatics 06-08-2010, 04:46 AM
Replies: 0
Views: 1,131
Posted By sanush
DE calculation for RNA Seq

Hi all
I am analyzing RNA seq data for DE. We have 2 groups (control & treatment) and sample in each group. We have calculated the RPKM values but not sure how to calculate the Fold change...
Forum: SOLiD 04-13-2010, 07:22 AM
Replies: 6
Views: 4,048
Posted By sanush
Hi Thanks for the reply. These are human...

Hi
Thanks for the reply. These are human cell line samples total RNA sample. We did double ribominus treatment to make sure 18s and 28s are removed. We checked it on bioanalyzer pico kit, but we...
Forum: SOLiD 04-12-2010, 12:54 PM
Replies: 6
Views: 4,048
Posted By sanush
Too many reads mapping towards intronic region

Hi all
We just finished our first RNA seq experiment in SOLiD platform and used partek to map our reads. We see that only 30% maps to exonic and remaining of our reads mapping to intronic and...
Forum: RNA Sequencing 04-12-2010, 08:58 AM
Replies: 1
Views: 1,943
Posted By sanush
Too many reads mapping towards intronic region

Hi all
We just finished our first RNA seq experiment in SOLiD platform and used partek to map our reads. We see that only 30% maps to exonic and remaining of our reads mapping to intronic...
Forum: RNA Sequencing 03-05-2010, 10:25 AM
Replies: 0
Views: 3,626
Posted By sanush
Bioanalyzer profile after ribominus treatment

Hi all
Could any you please send me a bioanalyzer profile after ribominus treatment for NGS. We are not sure about the profile after ribominus treatment

Thanks in advance
Sanush
Forum: SOLiD 12-03-2009, 06:44 AM
Replies: 3
Views: 3,208
Posted By sanush
Thanks Phillip I have that...

Thanks Phillip
I have that slide too, but it gives us a range 10 - 100 M. Is there any specifics like the number of mappable reads required for different applications... what...
Forum: SOLiD 12-02-2009, 12:59 PM
Replies: 3
Views: 3,208
Posted By sanush
Tag counts for RNA seq experiment

Hi all
We have to design an experiment to sequence the transcriptomes of 2 different cell types to know what genes are differentially expressed.

ABI recommends different Tag numbers...
Forum: SOLiD 12-01-2009, 07:19 AM
Replies: 6
Views: 2,967
Posted By sanush
Thanks for the suggestions. We aligned using full...

Thanks for the suggestions. We aligned using full length reads and not WT pipeline.

What % of your RNA remained after ribominus? Did you do one or two cycles of ribominus?

We started of with 5...
Forum: SOLiD 11-25-2009, 10:36 AM
Replies: 6
Views: 2,967
Posted By sanush
Hi Phillip, Thanks for the reply....

Hi Phillip,
Thanks for the reply. Here are some details about the experiment. We had 2 samples 1. Melanocyte and 2. Wistar Melanoma cell line. The RNA was isolated using Trizol method and...
Forum: RNA Sequencing 11-24-2009, 01:35 PM
Replies: 1
Views: 2,355
Posted By sanush
% matching problem- RNA_Seq

Hi
I am a new SOLiD user, and completed our first RNA-Seq experiment. I have a question regd the secondary analysis report. For the secondary analysis we uploaded whole human genome as reference...
Forum: SOLiD 11-24-2009, 09:54 AM
Replies: 6
Views: 2,967
Posted By sanush
New SOLiD user

Hi
I am a new SOLiD user, and completed our first RNA-Seq experiment. I have a question regd the secondary analysis report. For the secondary analysis we uploaded whole human genome as reference...
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