How useful are spike-in controls (like ERCC1 for example) for whole transcriptome RNA-seq in mouse or human?

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Has anyone used BGI Americas for an RNA-seq project and/or have a basis for comparison of different companies offering RNA-seq?

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How concerned should I be that a commercial "18S" rRNA primer pair actually recognizes the precursor RNA and not the mature one?

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How uniform is the microbiome of commercially sourced mice?

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02 March 2013 3,323 10 View

How small of a "fold-change" in gene expression can be reliably measured by RT-qPCR?

When using Sybr green or TaqMan qPCR assays to measure gene expression changes, can differences that are less than at least two-fold be taken as credible? What minimum fold-change or percent...

01 February 2013 1,682 44 View

For metagenomic "profiling" which is more useful, DGGE or TaqMan based qPCR?

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09 October 2012 6,265 16 View

What is the advantage of expressing an shRNA vs a microRNA primary transcript in a lentiviral vector?

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Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

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Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

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Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

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Has anyone used the Illumina ITS1 primer sets?

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How do you mesh a thin solid in Fluent?

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Errors in DNA sequences?

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Is it possible to define biogas as a fuel in the reformer process(scwg) in Homer software?

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I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

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What is the significance of (isolated) high titers of IgG anti GD1a antibodies in an older patient with polyneuropathy?

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Repository for capture-seq raw reads?

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Delphine Fagegaltier

This article addresses the pros and cons:

Synthetic spike-in standards for RNA-seq experiments.

Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B.javascript:

Genome Res. 2011 Sep;21(9):1543-51. Epub 2011 Aug 4.

PMID: 21816910 [PubMed - indexed for MEDLINE]

Seolkyoung Jung

It depends on the purpose. For me, it is useful to detect background noise of antisense transcription on strand-specific library and to estimate the detection limit of amount of transcripts in my experiment. But it is possible to affect the transcriptome sequencing results somehow.

David F. Barker

Interesting link:

http://cofactorgenomics.com/spike-controls-whats-take/?utm_medium=email&utm_campaign=Daily+Cofactor+Genomics&utm_content=Daily+Cofactor+Genomics+CID_c60717f2f01ad813efe7e91c3ba249bd&utm_source=Email+marketing+software&utm_term=Spike-in+controls++whats+your+take

Interesting assessment of Spike Ins, highlighting the necessity to find better sets in this article:

Article Normalization of RNA-seq data using factor analysis of contr...

Davide Risso

Just to be clear, our article refers specifically to the use of spike-ins for normalization.

Please, see this paper from NIST addressing the use of spike-ins for quality control:

http://www.nature.com/ncomms/2014/140925/ncomms6125/abs/ncomms6125.html