Does anybody know about published high-throughput mRNA expression data, with microRNA over-expression or knockdown vs. control experiments in HEK293 cells? It can be using any technology like micro arrays, RNA-seq, CAGE or other. Could you point to the paper and/or GEO accession?
Hi Nallasivam, Thanks for your answer, but this is not really miRNA knock-down or transfection vs. control.
Best,
Simon
Hi
Try the Gene Expression Atlas. A quick search with HEK293 as input gives a list of up and down genes. From these you can try getting the actual experiment and paper.
Check the link below for the search results
http://goo.gl/EjIsJ
GSE43574，Ribo-minus pair-end RNA-seq data
details see paper:http://www.ncbi.nlm.nih.gov/pubmed/23446348
Thanks for your answers, but these are not knock-down or over-expression experiments.
The gene expression atlas provides a comparative overview of gene expression of different cells and tissues.
I know the circular RNA paper and we have analyzed the the ribo-minus RNA-seq data set and it seems inconsistent with other RNA-seq data sets in the cell line.
I am looking for knockdown experiments like the Hafner et al. knockdown of 25 miRNA in HEK293 cell vs. mock transfection (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM538821), where they measured gene expression by Affymetrix Micro Arrays U133 2.0. I want to calculate differential expression following knock-down of the miRNA(s).
Doesn't sound like this is quite what you are looking for but this is a paper of knocking down the miRNA machinery, and subsequently looking at upregulated mRNAs. This doesn't give you the specific miRNAs involved but it may be able to indicate if any specific genes of interest are miRNA regulated in HEK293s.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635286/
Hi Jonathan,
Thanks for your answer, I know the paper and have analyzed these datasets. So it was very relevant, but I already know about.
Thanks,
Simon
Not sure if it is still of interest but this paper has just come out which may be of interest.
Best,
Jonathan
http://www.sciencedirect.com/science/article/pii/S0092867414013671#
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