Genome-wide study of the MSL1 effect on gene expression in Drosophila melanogaster
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Charles Girardot
PROVIDER: E-MTAB-3434 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The production of Tobacco Acid Pyrophosphatase (TAP), an enzyme commonly used for the removal of the 5â??cap of eukaryotic mRNAs, has been recently discontinued. Here we performed a comparison of current alternatives for the mapping of 5â??cap mRNAs and the associated transcription start sites in Sacharomyces cerevisiae. Specifically we compared TAP with Cap-clip and a Decapping Pyrophosphohydrolase. Our results suggest that Cap-clip is a good alternative for TAP. We used two biological replicates of S. cerevisiae that was grown to exponential phase (OD600 ~1) in rich media (YPAD). Samples where processed until the dephosphorylation step (CIP treatment). After that each sample was split in 4 aliquots: TAP treatment, Cap-Clip treatment, Decapping Pyrophosphohydrolase treatment or no treatment (negative control). From that step all samples are processed in parallel.
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Project description:This SuperSeries is composed of the following subset Series: GSE27452: Genome-wide maps of polyadenylation sites in control and PABPN1kd cells GSE32302: Genome-wide maps of polyadenylation sites in OPMD-model and control mice Refer to individual Series
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2014-06-20 | E-GEOD-51721 | biostudies-arrayexpress
Project description:Background Next Generation Sequencing technologies have facilitated differential gene expression analysis through RNA-seq and Tag-seq methods. RNA-seq has biases associated with transcript lengths, lacks uniform coverage of regions in mRNA and requires 10–20 times more reads than a typical Tag-seq. Most existing Tag-seq methods either have biases or not high throughput due to use of restriction enzymes or enzymatic manipulation of 5’ ends of mRNA or use of RNA ligations. Results We have developed EXpression Profiling through Randomly Sheared cDNA tag Sequencing (EXPRSS) that employs acoustic waves to randomly shear cDNA and generate sequence tags at a relatively defined position (~150-200 bp) from the 3′ end of each mRNA. Implementation of the method was verified through comparative analysis of expression data generated from EXPRSS, NlaIII-DGE and Affymetrix microarray and through qPCR quantification of selected genes. EXPRSS is a strand specific and restriction enzyme independent tag sequencing method that does not require cDNA length-based data transformations. EXPRSS is highly reproducible, is high-throughput and it also reveals alternative polyadenylation and polyadenylated antisense transcripts. It is cost-effective using barcoded multiplexing, avoids the biases of existing SAGE and derivative methods and can reveal polyadenylation position from paired-end sequencing. Conclusions EXPRSS Tag-seq provides sensitive and reliable gene expression data and enables high-throughput expression profiling with relatively simple downstream analysis. Five weeks old Arabidopsis (Col-0) leaf discs treated with water or flg22 for 60min; mRNA profiles were generated by deep sequencing on Illumina GAIIx using EXPRSS and NlaIII-DGE protocols, in quadruplicate.
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