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Title: Comparative Dynamic Transcriptome Analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation      
dateReleased:
03-28-2012
description:
Data was pre-processed array-wise using expresso (R/Bioconductor) with the RMA background correction method. We created our own probe annotation environment (cdf), which excludes probes in probesets that show cross-hybridization between Sc and Sp. 8708 annotated Sc probes and 13,317 annotated Sp probes out of a total of 120,855 probes showed cross-hybridization when a conservative intensity cut-off of 4.5 (log intensity values after preprocessing) was used. Cross-hybridizing probes were excluded from further analysis. This included 16 whole probe sets. Note that the standard GC-RMA method is not suitable for our purposes, since its bias model cannot handle bimodal intensity distributions, as caused by the simultaneous hybridization of Sc and Sp transcripts with global differences in RNA abundance. Labeling bias estimation and correction was done as described (Miller et al. 2011). Between-array normalization of arrays containing mixed Sc and Sp total RNA was done by proportional rescaling, such that the median Sp gene expression level was 1. Accordingly, between-array normalization of arrays containing mixed Sc and Sp labeled RNA was done by proportionally scaling the array to a median labeled Sp gene expression level of c. The constant c scales the median half-life of all experiments. We calibrated c in a way that the resulting median Sc wild-type mRNA half-life equaled that observed previously (Miller et al. 2011). Now, all Sc RNA levels, no matter if total or labeled, no matter from which experiment, can be compared on an absolute level. Decay rates and synthesis rates were obtained as described (Miller et al. 2011). The whole analysis workflow has been carried out using the open source R/Bioconductor package DTA
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-MTAB-760
refinement:
raw
keywords:
functional genomics
dateModified:
05-02-2014
creators:
Mai Sun
availability:
available
types:
gene expression
name:
cell comparison design, normalization test, metabolic labeling
ID:
A-AFFY-47
name:
Affymetrix GeneChip Yeast Genome 2.0 Array [Yeast_2]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-760/E-MTAB-760.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-760/E-MTAB-760.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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