Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models      
dateReleased:
04-01-2014
description:
Next-generation RNA-sequencing (RNA-seq) is rapidly emerging as the technology of choice for whole-transcriptome studies. However, RNA-seq is not a bias free technique. It requires large amounts of RNA and library preparation can introduce multiple artifacts, compounded by problems from later stages in the process. Nevertheless, RNA-seq is increasingly used in multiple studies, including the characterization of tissue-specific transcriptomes from invertebrate models of human disease. The generation of samples in this context is complex, involving the establishment of mutant strains and the delicate contamination prone process of dissecting the target tissue. Moreover, in order achieve the required amount of RNA, multiple samples need to be pooled. Such datasets pose extra challenges due to the large variability that may occur between similar pools, mostly due to the presence of cells from surrounding tissues. Therefore, in addition to standard quality control of RNA-seq data, analytical procedures for control of 'biological quality’ are critical for successful comparison of gene expression profiles. In this study, the transcriptome of the central nervous system of a Drosophila transgenic strain with neuronal-specific RNAi of a ubiquitous gene was profiled using RNA-seq. While conducting our investigation, we observed the existence of an unusual variance in the libraries and showed that the expression profile of a small panel of genes was sufficient to identify libraries with low levels of contamination from neighboring tissues, enabling the selection of a robust dataset for differential expression analysis. We additionally analyzed the potential of profiling a complex tissue to identify cell-type specific changes in response to target gene down-regulation. Finally, we demonstrated that trimming 5’ ends of reads decreases nucleotide frequency biases, increasing the coverage of protein coding genes with a potential positive impact in the incurrence of sampling errors. Central Nervous System profiles of third instar larvae WT (N=6), C24 (N=7), and X7/C24 D. melanogaster were generated by sequencing using the Illumina Hiseq2000.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-54724
refinement:
raw
alternateIdentifiers:
54724
keywords:
functional genomics
dateModified:
06-01-2014
availability:
available
types:
gene expression
name:
Drosophila melanogaster
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-54724/E-GEOD-54724.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-GEOD-54724/E-GEOD-54724.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54724
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
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

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.