Q-Pcr For Rna-Seq Data

Question

[Steffi]

Hey,

I know about the MAQC project which provides q-PCR data for approx. 1000 genes for human data. I wondered if there is also a similar data set around but for yeast instead of human? Additionally, I would be also interested in any other data set where qt-PCR data is available for a subset of the RNA-Seq data.

Thanks a lot for any suggestions, Stefanie

Answer 1

[Ahill]

Good question. Do you need raw RT-PCR amplification curves? This publication is human (not yeast) but it appears to include RNA-Seq data for two cell lines, plus corresponding RT-PCR relative quantitation for a subset of 27 transcripts:

Publication: http://nar.oxfordjournals.org/content/39/2/e9.full

Raw RNA-seq reads for the cell lines MKN28, MKN45 at this site: http://neuma.kobic.re.kr/

RT-PCR results for 27 selected transcripts in the same 2 cell lines are in Supplemental Table 1: http://nar.oxfordjournals.org/content/suppl/2010/10/13/gkq1015.DC1/nar-01921-met-g-2010-File009.pdf

Answer 2

[Malachi Griffith]

Another set of q-PCR data used for validation of human RNA-seq results is described in: Griffith et al.. Exon specific qPCRs were designed for ~200 genes. These exons were found to be differentially or alternatively expressed between a pair of cell lines.

The RNA-seq data was generated for a single replicate from each cell line. The qPCR data was generated for biological triplicates (and each of these had technical triplicates).

The raw data can be downloaded here: ValidationResultsPackage.zip